rs2687481

Variant names:

• chr7-126229068-G-T
• rs2687481
• ENST00000809641.1:n.145-4469G>T

Variant summary

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

The ENST00000809641.1(ENSG00000305210):​n.145-4469G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,020 control chromosomes in the GnomAD database, including 5,564 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 0.26 (5564 hom., cov: 33)
• Consequence: ENSG00000305210 ENST00000809641.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 5 publications found

Genes affected

ENSG00000305210 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809641.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305210	ENST00000809641.1		n.145-4469G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39033 AN: 151902 Hom.: 5560 Cov.: 33

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.257 AC: 39064 AN: 152020 Hom.: 5564 Cov.: 33 AF XY: 0.260 AC XY: 19330 AN XY: 74288

African (AFR) AF: 0.375 AC: 15555 AN: 41464

American (AMR) AF: 0.212 AC: 3239 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 691 AN: 3472

East Asian (EAS) AF: 0.231 AC: 1195 AN: 5162

South Asian (SAS) AF: 0.171 AC: 824 AN: 4816

European-Finnish (FIN) AF: 0.346 AC: 3650 AN: 10542

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13174 AN: 67976

Other (OTH) AF: 0.235 AC: 496 AN: 2110

Alfa AF: 0.210 Hom.: 4487

Bravo AF: 0.256

Asia WGS AF: 0.215 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.3
DANN	Benign	0.54
PhyloP100		1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2687481;

hg19: chr7-125869122;