6-137553271-A-G

Position:

• chr6-137553271-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.446

Alfa AF: 0.460 Hom.: 26884

Bravo AF: 0.408

Asia WGS AF: 0.552 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9321619; hg19: chr6-137874408;