6-19990741-G-T

Variant names:

• chr6-19990741-G-T
• rs965037

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 0.671 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.802 AC: 33280 AN: 41474

American (AMR) AF: 0.669 AC: 10206 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1938 AN: 3470

East Asian (EAS) AF: 0.808 AC: 4168 AN: 5160

South Asian (SAS) AF: 0.613 AC: 2951 AN: 4814

European-Finnish (FIN) AF: 0.576 AC: 6031 AN: 10476

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.607 AC: 41221 AN: 67876

Other (OTH) AF: 0.633 AC: 1334 AN: 2106

Alfa AF: 0.628 Hom.: 117275

Bravo AF: 0.686

Asia WGS AF: 0.692 AC: 2388 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.22
DANN	Benign	0.21
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs965037; hg19: chr6-19990972;