chr6-6930777-G-A

Variant names:

• chr6-6930777-G-A
• rs1536242

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 0.24 in 151,950 control chromosomes in the GnomAD database, including 4,645 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 0.24 (4645 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36446 AN: 151832 Hom.: 4637 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.240 AC: 36480 AN: 151950 Hom.: 4645 Cov.: 32 AF XY: 0.243 AC XY: 18048 AN XY: 74262

African (AFR) AF: 0.272 AC: 11280 AN: 41418

American (AMR) AF: 0.278 AC: 4242 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 573 AN: 3468

East Asian (EAS) AF: 0.495 AC: 2535 AN: 5120

South Asian (SAS) AF: 0.246 AC: 1186 AN: 4812

European-Finnish (FIN) AF: 0.200 AC: 2115 AN: 10570

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13946 AN: 67980

Other (OTH) AF: 0.202 AC: 426 AN: 2106

Alfa AF: 0.212 Hom.: 2476

Bravo AF: 0.252

Asia WGS AF: 0.319 AC: 1106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.027
DANN	Benign	0.39
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1536242; hg19: chr6-6931010;