ENST00000512237.1:n.89+6056C>T

Variant names:

• chr5-92660992-C-T
• rs17664587
• ENST00000512237.1:n.89+6056C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000512237.1(ENSG00000249169):​n.89+6056C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0352 in 151,670 control chromosomes in the GnomAD database, including 119 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.035 (119 hom., cov: 32)
  • Exomes 𝑓: 0.028 (0 hom.)
• Consequence: ENSG00000249169 ENST00000512237.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.651
• Publications: 1 publications found

Genes affected

ENSG00000249169 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0352 (5344/151634) while in subpopulation NFE AF = 0.0495 (3349/67656). AF 95% confidence interval is 0.0481. There are 119 homozygotes in GnomAd4. There are 2493 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 119 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512237.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105379082	NR_188296.1		n.362+8760G>A		intron	N/A
	LOC105379082	NR_188297.1		n.217+10492G>A		intron	N/A
	LOC105379082	NR_188298.1		n.217+10492G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249169	ENST00000512237.1	TSL:3	n.89+6056C>T		intron	N/A
	ENSG00000249776	ENST00000718057.1		n.390+8760G>A		intron	N/A
	ENSG00000249776	ENST00000850101.1		n.256+10492G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0353 AC: 5346 AN: 151516 Hom.: 119 Cov.: 32

Gnomad AFR AF: 0.0144

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0407

Gnomad ASJ AF: 0.0560

Gnomad EAS AF: 0.000389

Gnomad SAS AF: 0.0315

Gnomad FIN AF: 0.0278

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0495

Gnomad OTH AF: 0.0374

GnomAD4 exome AF: 0.0278 AC: 1 AN: 36 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 14

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0278 AC: 1 AN: 36

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0352 AC: 5344 AN: 151634 Hom.: 119 Cov.: 32 AF XY: 0.0337 AC XY: 2493 AN XY: 74080

African (AFR) AF: 0.0144 AC: 597 AN: 41464

American (AMR) AF: 0.0407 AC: 617 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.0560 AC: 194 AN: 3464

East Asian (EAS) AF: 0.000390 AC: 2 AN: 5124

South Asian (SAS) AF: 0.0315 AC: 152 AN: 4828

European-Finnish (FIN) AF: 0.0278 AC: 295 AN: 10610

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0495 AC: 3349 AN: 67656

Other (OTH) AF: 0.0366 AC: 77 AN: 2106

Alfa AF: 0.0459 Hom.: 301

Bravo AF: 0.0357

Asia WGS AF: 0.0120 AC: 42 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.5
DANN	Benign	0.56
PhyloP100		0.65
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17664587; hg19: chr5-91996699;