rs6964969

Variant names:

• chr7-50405553-A-G
• rs6964969

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 0.234 in 148,414 control chromosomes in the GnomAD database, including 4,542 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 0.23 (4542 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519
• Publications: 22 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 (SAS) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.234 AC: 34760 AN: 148296 Hom.: 4538 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.0893

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.234 AC: 34785 AN: 148414 Hom.: 4542 Cov.: 32 AF XY: 0.235 AC XY: 16918 AN XY: 72124

African (AFR) AF: 0.191 AC: 7904 AN: 41294

American (AMR) AF: 0.236 AC: 3570 AN: 15096

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 728 AN: 3402

East Asian (EAS) AF: 0.0895 AC: 450 AN: 5028

South Asian (SAS) AF: 0.265 AC: 1225 AN: 4622

European-Finnish (FIN) AF: 0.281 AC: 2665 AN: 9484

Middle Eastern (MID) AF: 0.293 AC: 85 AN: 290

European-Non Finnish (NFE) AF: 0.263 AC: 17404 AN: 66238

Other (OTH) AF: 0.239 AC: 490 AN: 2052

Alfa AF: 0.252 Hom.: 8171

Bravo AF: 0.237

Asia WGS AF: 0.172 AC: 599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.48
DANN	Benign	0.44
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs6964969; hg19: chr7-50473251;