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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000764443.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228683	ENST00000764443.1		n.444+1996G>A		intron	N/A
	ENSG00000228683	ENST00000764444.1		n.425+1996G>A		intron	N/A
	ENSG00000228683	ENST00000764445.1		n.76+1996G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs35648;

hg19: chr10-80501859;