6-19863934-G-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;