6-137649927-T-G

Variant names:

• chr6-137649927-T-G
• rs928720

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 0.433 in 151,776 control chromosomes in the GnomAD database, including 14,391 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 (14391 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65739 AN: 151658 Hom.: 14386 Cov.: 30

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.433 AC: 65760 AN: 151776 Hom.: 14391 Cov.: 30 AF XY: 0.437 AC XY: 32423 AN XY: 74162

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.449

Alfa AF: 0.389 Hom.: 2412

Bravo AF: 0.422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs928720; hg19: chr6-137971064;