rs2501677

Variant names:

• chr10-6904790-A-T
• rs2501677
• ENST00000457632.1:n.45-12833T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000457632.1(ENSG00000287277):​n.45-12833T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0693 in 152,234 control chromosomes in the GnomAD database, including 457 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 0.069 (457 hom., cov: 32)
• Consequence: ENSG00000287277 ENST00000457632.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.674
• Publications: 8 publications found

Genes affected

ENSG00000287277 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376387	NR_188183.1	n.568+30323T>A		intron_variant	Intron 3 of 4
LOC105376387	NR_188184.1	n.370+30323T>A		intron_variant	Intron 2 of 4
LOC105376387	NR_188185.1	n.370+30323T>A		intron_variant	Intron 2 of 4
LOC105376387	NR_188186.1	n.370+30323T>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287277	ENST00000457632.1	n.45-12833T>A		intron_variant	Intron 1 of 2	3
ENSG00000287277	ENST00000652889.2	n.419+30323T>A		intron_variant	Intron 2 of 3
ENSG00000287277	ENST00000654694.1	n.376+30323T>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0693 AC: 10538 AN: 152116 Hom.: 457 Cov.: 32

Gnomad AFR AF: 0.0283

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0785

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.0723

Gnomad FIN AF: 0.0525

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.0896

Gnomad OTH AF: 0.0785

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0693 AC: 10550 AN: 152234 Hom.: 457 Cov.: 32 AF XY: 0.0681 AC XY: 5069 AN XY: 74428

African (AFR) AF: 0.0285 AC: 1184 AN: 41560

American (AMR) AF: 0.0785 AC: 1201 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3468

East Asian (EAS) AF: 0.145 AC: 751 AN: 5176

South Asian (SAS) AF: 0.0724 AC: 349 AN: 4820

European-Finnish (FIN) AF: 0.0525 AC: 556 AN: 10600

Middle Eastern (MID) AF: 0.0342 AC: 10 AN: 292

European-Non Finnish (NFE) AF: 0.0896 AC: 6090 AN: 68004

Other (OTH) AF: 0.0777 AC: 164 AN: 2110

Alfa AF: 0.0860 Hom.: 337

Bravo AF: 0.0695

Asia WGS AF: 0.102 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.38
DANN	Benign	0.76
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs2501677; hg19: chr10-6946752;