rs2692877

Variant names:

• chr7-109701895-G-A
• rs2692877
• ENST00000830489.1:n.355+14534C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-109701895-G-A
• chr7-109701895-G-T

Variant summary

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

The ENST00000830489.1(ENSG00000308019):​n.355+14534C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 151,730 control chromosomes in the GnomAD database, including 18,940 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 0.50 (18940 hom., cov: 32)
• Consequence: ENSG00000308019 ENST00000830489.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762
• Publications: 2 publications found

Genes affected

ENSG00000308019 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308019	ENST00000830489.1	n.355+14534C>T		intron_variant	Intron 3 of 3
ENSG00000308019	ENST00000830490.1	n.343+14534C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75111 AN: 151612 Hom.: 18911 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.496 AC: 75192 AN: 151730 Hom.: 18940 Cov.: 32 AF XY: 0.498 AC XY: 36922 AN XY: 74110

African (AFR) AF: 0.572 AC: 23708 AN: 41422

American (AMR) AF: 0.420 AC: 6386 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1853 AN: 3466

East Asian (EAS) AF: 0.596 AC: 3070 AN: 5152

South Asian (SAS) AF: 0.593 AC: 2859 AN: 4818

European-Finnish (FIN) AF: 0.504 AC: 5308 AN: 10530

Middle Eastern (MID) AF: 0.521 AC: 151 AN: 290

European-Non Finnish (NFE) AF: 0.448 AC: 30357 AN: 67830

Other (OTH) AF: 0.484 AC: 1017 AN: 2102

Alfa AF: 0.475 Hom.: 5310

Bravo AF: 0.488

Asia WGS AF: 0.594 AC: 2063 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.2
DANN	Benign	0.52
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs2692877; hg19: chr7-109341952;