17-44349083-A-G

Variant names:

• chr17-44349083-A-G
• rs187491758
• NM_002087.4:c.-7-75A>G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The NM_002087.4(GRN):​c.-7-75A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00114 in 1,519,704 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0061 (4 hom., cov: 33)
  • Exomes 𝑓: 0.00058 (9 hom.)
• Consequence: GRN NM_002087.4 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.258

Genes affected

GRN (HGNC:4601): (granulin precursor) Granulins are a family of secreted, glycosylated peptides that are cleaved from a single precursor protein with 7.5 repeats of a highly conserved 12-cysteine granulin/epithelin motif. The 88 kDa precursor protein, progranulin, is also called proepithelin and PC cell-derived growth factor. Cleavage of the signal peptide produces mature granulin which can be further cleaved into a variety of active, 6 kDa peptides. These smaller cleavage products are named granulin A, granulin B, granulin C, etc. Epithelins 1 and 2 are synonymous with granulins A and B, respectively. Both the peptides and intact granulin protein regulate cell growth. However, different members of the granulin protein family may act as inhibitors, stimulators, or have dual actions on cell growth. Granulin family members are important in normal development, wound healing, and tumorigenesis. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 17-44349083-A-G is Benign according to our data. Variant chr17-44349083-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1197342.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00613 (934/152338) while in subpopulation AFR AF = 0.0215 (895/41574). AF 95% confidence interval is 0.0204. There are 4 homozygotes in GnomAd4. There are 429 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position FAILED quality control check.
• BS2: High Homozygotes in GnomAd4 at 4 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRN	NM_002087.4	c.-7-75A>G		intron_variant	Intron 1 of 12	ENST00000053867.8	NP_002078.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRN	ENST00000053867.8	c.-7-75A>G		intron_variant	Intron 1 of 12	1	NM_002087.4	ENSP00000053867.2

Frequencies

GnomAD3 genomes AF: 0.00610 AC: 929 AN: 152220 Hom.: 4 Cov.: 33

Gnomad AFR AF: 0.0215

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00150

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00526

GnomAD4 exome AF: 0.000584 AC: 799 AN: 1367366 Hom.: 9 AF XY: 0.000477 AC XY: 327 AN XY: 685038

Gnomad4 AFR exome AF: 0.0206 AC: 652 AN: 31674

Gnomad4 AMR exome AF: 0.00123 AC: 55 AN: 44610

Gnomad4 ASJ exome AF: 0.00 AC: 0 AN: 25522

Gnomad4 EAS exome AF: 0.00 AC: 0 AN: 39312

Gnomad4 SAS exome AF: 0.0000237 AC: 2 AN: 84464

Gnomad4 FIN exome AF: 0.00 AC: 0 AN: 46468

Gnomad4 NFE exome AF: 0.00000969 AC: 10 AN: 1032448

Gnomad4 Remaining exome AF: 0.00134 AC: 77 AN: 57392

GnomAD4 genome AF: 0.00613 AC: 934 AN: 152338 Hom.: 4 Cov.: 33 AF XY: 0.00576 AC XY: 429 AN XY: 74488

Gnomad4 AFR AF: 0.0215 AC: 0.0215279 AN: 0.0215279

Gnomad4 AMR AF: 0.00150 AC: 0.00150248 AN: 0.00150248

Gnomad4 ASJ AF: 0.00 AC: 0 AN: 0

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.000207 AC: 0.000207039 AN: 0.000207039

Gnomad4 FIN AF: 0.00 AC: 0 AN: 0

Gnomad4 NFE AF: 0.0000441 AC: 0.0000441021 AN: 0.0000441021

Gnomad4 OTH AF: 0.00520 AC: 0.00520341 AN: 0.00520341

Alfa AF: 0.0123 Hom.: 1

Bravo AF: 0.00653

Asia WGS AF: 0.00115 AC: 4 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Feb 26, 2020

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.36
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs187491758; hg19: chr17-42426451;