6-19990741-G-T

Variant names:

• chr6-19990741-G-T
• rs965037

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 0.671 in 151,828 control chromosomes in the GnomAD database, including 34,834 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 0.67 (34834 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 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: 0.670 AC: 101708 AN: 151710 Hom.: 34784 Cov.: 31

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.671 AC: 101821 AN: 151828 Hom.: 34834 Cov.: 31 AF XY: 0.668 AC XY: 49511 AN XY: 74160

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.633

Alfa AF: 0.617 Hom.: 50029

Bravo AF: 0.686

Asia WGS AF: 0.692 AC: 2388 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.22
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs965037; hg19: chr6-19990972;