10-78742102-C-T

Variant names:

• chr10-78742102-C-T
• rs35648
• ENST00000764443.1:n.444+1996G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000764443.1(ENSG00000228683):​n.444+1996G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 152,102 control chromosomes in the GnomAD database, including 40,529 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 0.71 (40529 hom., cov: 32)
• Consequence: ENSG00000228683 ENST00000764443.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.90
• Publications: 5 publications found

Genes affected

ENSG00000228683 (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 (NFE) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378379	XR_946100.2	n.446+1996G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228683	ENST00000764443.1	n.444+1996G>A		intron_variant	Intron 1 of 3
ENSG00000228683	ENST00000764444.1	n.425+1996G>A		intron_variant	Intron 1 of 2
ENSG00000228683	ENST00000764445.1	n.76+1996G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107599 AN: 151984 Hom.: 40545 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.925

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.707 AC: 107612 AN: 152102 Hom.: 40529 Cov.: 32 AF XY: 0.705 AC XY: 52415 AN XY: 74362

African (AFR) AF: 0.422 AC: 17483 AN: 41454

American (AMR) AF: 0.780 AC: 11939 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 2930 AN: 3470

East Asian (EAS) AF: 0.719 AC: 3711 AN: 5164

South Asian (SAS) AF: 0.789 AC: 3799 AN: 4818

European-Finnish (FIN) AF: 0.751 AC: 7958 AN: 10592

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.842 AC: 57234 AN: 67996

Other (OTH) AF: 0.714 AC: 1503 AN: 2106

Alfa AF: 0.804 Hom.: 31548

Bravo AF: 0.698

Asia WGS AF: 0.720 AC: 2508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.016
DANN	Benign	0.16
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs35648; hg19: chr10-80501859;