rs8102683

Positions:

• chr19-40857860-T-C

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 0.75 in 150,876 control chromosomes in the GnomAD database, including 43,364 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 0.75 (43364 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 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: 0.750 AC: 113148 AN: 150764 Hom.: 43329 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.750 AC: 113226 AN: 150876 Hom.: 43364 Cov.: 32 AF XY: 0.750 AC XY: 55251 AN XY: 73640

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.755

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.629

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.728

Alfa AF: 0.737 Hom.: 44822

Bravo AF: 0.749

Asia WGS AF: 0.706 AC: 2418 AN: 3428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.46

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs8102683; hg19: chr19-41363765;