6-153973938-A-G

Variant names:

• chr6-153973938-A-G
• rs7760028

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 0.182 in 152,022 control chromosomes in the GnomAD database, including 2,777 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 0.18 (2777 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626
• Publications: 2 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 (SAS) allele frequency at 95% confidence interval = 0.352 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: 0.182 AC: 27635 AN: 151904 Hom.: 2776 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.182 AC: 27633 AN: 152022 Hom.: 2777 Cov.: 32 AF XY: 0.191 AC XY: 14231 AN XY: 74332

African (AFR) AF: 0.106 AC: 4410 AN: 41462

American (AMR) AF: 0.251 AC: 3822 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 781 AN: 3472

East Asian (EAS) AF: 0.336 AC: 1738 AN: 5176

South Asian (SAS) AF: 0.366 AC: 1766 AN: 4826

European-Finnish (FIN) AF: 0.231 AC: 2436 AN: 10558

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12040 AN: 67972

Other (OTH) AF: 0.186 AC: 390 AN: 2102

Alfa AF: 0.175 Hom.: 326

Bravo AF: 0.173

Asia WGS AF: 0.360 AC: 1253 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	0.22
DANN	Benign	0.23
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs7760028; hg19: chr6-154295073;