rs4934256

Variant names:

• chr10-86740608-A-G
• rs4934256
• ENST00000740897.1:n.526+15143T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-86740608-A-G
• chr10-86740608-A-T

Variant summary

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

The ENST00000740897.1(ENSG00000272631):​n.526+15143T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0554 in 151,710 control chromosomes in the GnomAD database, including 345 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 0.055 (345 hom., cov: 29)
• Consequence: ENSG00000272631 ENST00000740897.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 3 publications found

Genes affected

ENSG00000272631 (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 (NFE) allele frequency at 95% confidence interval = 0.0711 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000740897.1. 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
	ENSG00000272631	ENST00000740897.1		n.526+15143T>C		intron	N/A
	ENSG00000272631	ENST00000740898.1		n.230+15433T>C		intron	N/A
	ENSG00000272631	ENST00000740899.1		n.202-3967T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0555 AC: 8409 AN: 151592 Hom.: 345 Cov.: 29

Gnomad AFR AF: 0.0180

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.0419

Gnomad ASJ AF: 0.0280

Gnomad EAS AF: 0.0232

Gnomad SAS AF: 0.0327

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.0728

Gnomad OTH AF: 0.0594

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

GnomAD4 genome AF: 0.0554 AC: 8410 AN: 151710 Hom.: 345 Cov.: 29 AF XY: 0.0570 AC XY: 4228 AN XY: 74124

African (AFR) AF: 0.0181 AC: 751 AN: 41408

American (AMR) AF: 0.0418 AC: 637 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.0280 AC: 97 AN: 3464

East Asian (EAS) AF: 0.0226 AC: 115 AN: 5082

South Asian (SAS) AF: 0.0318 AC: 153 AN: 4804

European-Finnish (FIN) AF: 0.139 AC: 1453 AN: 10482

Middle Eastern (MID) AF: 0.0308 AC: 9 AN: 292

European-Non Finnish (NFE) AF: 0.0728 AC: 4948 AN: 67930

Other (OTH) AF: 0.0588 AC: 124 AN: 2108

Alfa AF: 0.0600 Hom.: 43

Bravo AF: 0.0477

Asia WGS AF: 0.0450 AC: 158 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	0.30
DANN	Benign	0.30
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4934256; hg19: chr10-88500365;