rs2242071

Positions:

• chr2-208129973-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Moderate BP6_Moderate BA1

The NR_038437.1(LOC100507443):​n.98-7083C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 780,104 control chromosomes in the GnomAD database, including 204,984 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.72 (39520 hom., cov: 32)
  • Exomes 𝑓: 0.72 (165464 hom.)
• Consequence: LOC100507443 NR_038437.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.628

Genes affected

LOC100507443 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BP6: Variant 2-208129973-C-T is Benign according to our data. Variant chr2-208129973-C-T is described in ClinVar as [Benign]. Clinvar id is 1291617.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100507443	NR_038437.1	n.98-7083C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109099 AN: 151982 Hom.: 39478 Cov.: 32

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.710

GnomAD4 exome AF: 0.721 AC: 452796 AN: 628004 Hom.: 165464 AF XY: 0.723 AC XY: 243845 AN XY: 337154

Gnomad4 AFR exome AF: 0.714

Gnomad4 AMR exome AF: 0.556

Gnomad4 ASJ exome AF: 0.728

Gnomad4 EAS exome AF: 0.505

Gnomad4 SAS exome AF: 0.714

Gnomad4 FIN exome AF: 0.753

Gnomad4 NFE exome AF: 0.753

Gnomad4 OTH exome AF: 0.717

GnomAD4 genome AF: 0.718 AC: 109198 AN: 152100 Hom.: 39520 Cov.: 32 AF XY: 0.715 AC XY: 53176 AN XY: 74348

Gnomad4 AFR AF: 0.718

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.702

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.711

Alfa AF: 0.736 Hom.: 42619

Bravo AF: 0.705

Asia WGS AF: 0.607 AC: 2114 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	15
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2242071; hg19: chr2-208994697; COSMIC: COSV56408336;