6-19990812-G-T

Variant names:

• chr6-19990812-G-T
• rs965036

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 0.756 in 151,942 control chromosomes in the GnomAD database, including 43,622 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 0.76 (43622 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 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: 0.755 AC: 114688 AN: 151824 Hom.: 43570 Cov.: 31

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.756 AC: 114802 AN: 151942 Hom.: 43622 Cov.: 31 AF XY: 0.754 AC XY: 55993 AN XY: 74230

African (AFR) AF: 0.824 AC: 34165 AN: 41456

American (AMR) AF: 0.759 AC: 11593 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2096 AN: 3468

East Asian (EAS) AF: 0.810 AC: 4176 AN: 5158

South Asian (SAS) AF: 0.660 AC: 3182 AN: 4818

European-Finnish (FIN) AF: 0.752 AC: 7911 AN: 10526

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49277 AN: 67926

Other (OTH) AF: 0.739 AC: 1561 AN: 2112

Alfa AF: 0.729 Hom.: 20642

Bravo AF: 0.763

Asia WGS AF: 0.729 AC: 2517 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.28
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs965036;

hg19: chr6-19991043;