chr7-6406396-A-G

Variant names:

• chr7-6406396-A-G
• rs10951983

Variant summary

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

The variant allele was found at a frequency of 0.149 in 150,294 control chromosomes in the GnomAD database, including 2,097 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 0.15 (2097 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 23 publications found

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 (NFE) allele frequency at 95% confidence interval = 0.215 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: 0.149 AC: 22316 AN: 150172 Hom.: 2094 Cov.: 32

Gnomad AFR AF: 0.0447

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0919

Gnomad EAS AF: 0.0683

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.149 AC: 22327 AN: 150294 Hom.: 2097 Cov.: 32 AF XY: 0.144 AC XY: 10569 AN XY: 73208

African (AFR) AF: 0.0448 AC: 1859 AN: 41500

American (AMR) AF: 0.150 AC: 2212 AN: 14744

Ashkenazi Jewish (ASJ) AF: 0.0919 AC: 319 AN: 3472

East Asian (EAS) AF: 0.0687 AC: 291 AN: 4234

South Asian (SAS) AF: 0.112 AC: 534 AN: 4780

European-Finnish (FIN) AF: 0.182 AC: 1878 AN: 10326

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14839 AN: 67942

Other (OTH) AF: 0.136 AC: 285 AN: 2090

Alfa AF: 0.188 Hom.: 1921

Bravo AF: 0.144

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.0
DANN	Benign	0.68
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs10951983; hg19: chr7-6446027;