6-61177350-A-G

Variant names:

• chr6-61177350-A-G
• rs977382

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 0.267 in 152,026 control chromosomes in the GnomAD database, including 6,831 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 0.27 (6831 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.569
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40588 AN: 151908 Hom.: 6826 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0498

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.267 AC: 40622 AN: 152026 Hom.: 6831 Cov.: 32 AF XY: 0.257 AC XY: 19070 AN XY: 74326

African (AFR) AF: 0.477 AC: 19745 AN: 41426

American (AMR) AF: 0.203 AC: 3103 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3466

East Asian (EAS) AF: 0.0497 AC: 258 AN: 5186

South Asian (SAS) AF: 0.104 AC: 501 AN: 4828

European-Finnish (FIN) AF: 0.134 AC: 1427 AN: 10610

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14381 AN: 67936

Other (OTH) AF: 0.220 AC: 464 AN: 2110

Alfa AF: 0.175 Hom.: 696

Bravo AF: 0.284

Asia WGS AF: 0.117 AC: 408 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.66
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs977382; hg19: chr6-62060364;