6-19863934-G-T

Variant names:

• chr6-19863934-G-T
• rs1011119

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 0.652 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.652 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

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.859

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.657

Alfa AF: 0.603 Hom.: 4062

Bravo AF: 0.653

Asia WGS AF: 0.711 AC: 2470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1011119; hg19: chr6-19864165;