chr19-40857860-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 33 publications found

Genes affected

ENSG00000268797 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000601627.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000268797	ENST00000601627.1	TSL:3	n.118-34131T>C		intron	N/A	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

African (AFR) AF: 0.747 AC: 30701 AN: 41120

American (AMR) AF: 0.755 AC: 11447 AN: 15156

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2548 AN: 3462

East Asian (EAS) AF: 0.780 AC: 3858 AN: 4948

South Asian (SAS) AF: 0.629 AC: 2986 AN: 4750

European-Finnish (FIN) AF: 0.847 AC: 8799 AN: 10394

Middle Eastern (MID) AF: 0.721 AC: 209 AN: 290

European-Non Finnish (NFE) AF: 0.745 AC: 50513 AN: 67772

Other (OTH) AF: 0.728 AC: 1510 AN: 2074

Alfa AF: 0.739 Hom.: 54771

Bravo AF: 0.749

Asia WGS AF: 0.706 AC: 2418 AN: 3428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.46
PhyloP100		-0.19

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

Other links and lift over

dbSNP: rs8102683; hg19: chr19-41363765;