rs6467410

Variant names:

• chr7-131999774-T-A
• rs6467410

Your query was ambiguous. Multiple possible variants found:

• chr7-131999774-T-A
• chr7-131999774-T-C
• chr7-131999774-T-G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.868 in 152,218 control chromosomes in the GnomAD database, including 57,637 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 0.87 (57637 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.77
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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

Frequencies

GnomAD3 genomes AF: 0.868 AC: 132074 AN: 152100 Hom.: 57573 Cov.: 32

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.868 AC: 132201 AN: 152218 Hom.: 57637 Cov.: 32 AF XY: 0.870 AC XY: 64710 AN XY: 74402

African (AFR) AF: 0.922 AC: 38285 AN: 41546

American (AMR) AF: 0.882 AC: 13490 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2757 AN: 3470

East Asian (EAS) AF: 0.984 AC: 5072 AN: 5154

South Asian (SAS) AF: 0.908 AC: 4372 AN: 4814

European-Finnish (FIN) AF: 0.848 AC: 8983 AN: 10590

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.831 AC: 56511 AN: 68024

Other (OTH) AF: 0.854 AC: 1805 AN: 2114

Alfa AF: 0.854 Hom.: 6904

Bravo AF: 0.873

Asia WGS AF: 0.939 AC: 3263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	14
DANN	Benign	0.72
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs6467410; hg19: chr7-131684533;