rs8102683

Variant names:

• chr19-40857860-T-C
• rs8102683
• ENST00000601627.1:n.118-34131T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000601627.1(ENSG00000268797):​n.118-34131T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000268797 ENST00000601627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187

Genes affected

ENSG00000268797 (HGNC:):

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000268797	ENST00000601627.1	n.118-34131T>C		intron_variant	Intron 1 of 3	3		ENSP00000469533.1

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;