6-19863934-G-T

Variant names:

• chr6-19863934-G-T
• rs1011119

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 0.652 in 152,028 control chromosomes in the GnomAD database, including 32,432 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 0.65 (32432 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.550
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99026 AN: 151912 Hom.: 32409 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.652 AC: 99107 AN: 152028 Hom.: 32432 Cov.: 32 AF XY: 0.651 AC XY: 48375 AN XY: 74310

African (AFR) AF: 0.659 AC: 27324 AN: 41460

American (AMR) AF: 0.640 AC: 9778 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2062 AN: 3472

East Asian (EAS) AF: 0.859 AC: 4437 AN: 5168

South Asian (SAS) AF: 0.632 AC: 3049 AN: 4822

European-Finnish (FIN) AF: 0.615 AC: 6488 AN: 10558

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.645 AC: 43846 AN: 67956

Other (OTH) AF: 0.657 AC: 1387 AN: 2112

Alfa AF: 0.633 Hom.: 9653

Bravo AF: 0.653

Asia WGS AF: 0.711 AC: 2470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	14
DANN	Benign	0.78
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs1011119; hg19: chr6-19864165;