10-83885745-G-T

Variant names:

• chr10-83885745-G-T
• rs7906586
• ENST00000740261.1:n.1162+1271C>A

Variant summary

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

The ENST00000740261.1(ENSG00000296548):​n.1162+1271C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,834 control chromosomes in the GnomAD database, including 27,677 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 0.60 (27677 hom., cov: 31)
• Consequence: ENSG00000296548 ENST00000740261.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 4 publications found

Genes affected

ENSG00000296548 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000740261.1. 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
	ENSG00000296548	ENST00000740261.1		n.1162+1271C>A		intron	N/A
	ENSG00000296548	ENST00000740263.1		n.294-906C>A		intron	N/A
	ENSG00000296548	ENST00000740264.1		n.119+1271C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90887 AN: 151714 Hom.: 27637 Cov.: 31

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.599 AC: 90980 AN: 151834 Hom.: 27677 Cov.: 31 AF XY: 0.603 AC XY: 44737 AN XY: 74198

African (AFR) AF: 0.541 AC: 22379 AN: 41364

American (AMR) AF: 0.690 AC: 10538 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1994 AN: 3468

East Asian (EAS) AF: 0.894 AC: 4609 AN: 5158

South Asian (SAS) AF: 0.686 AC: 3303 AN: 4812

European-Finnish (FIN) AF: 0.563 AC: 5928 AN: 10528

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40285 AN: 67922

Other (OTH) AF: 0.630 AC: 1330 AN: 2112

Alfa AF: 0.594 Hom.: 41352

Bravo AF: 0.607

Asia WGS AF: 0.773 AC: 2689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.39
DANN	Benign	0.22
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs7906586; hg19: chr10-85645501;