6-137553271-A-G

Variant names:

• chr6-137553271-A-G
• rs9321619

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 0.428 in 152,072 control chromosomes in the GnomAD database, including 14,986 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 0.43 (14986 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 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: 0.428 AC: 65110 AN: 151954 Hom.: 14977 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.428 AC: 65153 AN: 152072 Hom.: 14986 Cov.: 32 AF XY: 0.438 AC XY: 32536 AN XY: 74356

African (AFR) AF: 0.259 AC: 10734 AN: 41506

American (AMR) AF: 0.461 AC: 7039 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1288 AN: 3470

East Asian (EAS) AF: 0.616 AC: 3185 AN: 5174

South Asian (SAS) AF: 0.558 AC: 2691 AN: 4820

European-Finnish (FIN) AF: 0.637 AC: 6732 AN: 10564

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 32013 AN: 67946

Other (OTH) AF: 0.446 AC: 940 AN: 2106

Alfa AF: 0.454 Hom.: 61174

Bravo AF: 0.408

Asia WGS AF: 0.552 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.8
DANN	Benign	0.78
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs9321619; hg19: chr6-137874408;