rs734241

Variant names:

• chr10-113479843-G-A
• rs734241
• ENST00000793155.1:n.82+234G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-113479843-G-A
• chr10-113479843-G-C
• chr10-113479843-G-T

Variant summary

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

The ENST00000793155.1(ENSG00000303244):​n.82+234G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,170 control chromosomes in the GnomAD database, including 2,084 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 0.12 (2084 hom., cov: 33)
• Consequence: ENSG00000303244 ENST00000793155.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.684
• Publications: 9 publications found

Genes affected

ENSG00000303244 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793155.1. 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
	ENSG00000303244	ENST00000793155.1		n.82+234G>A		intron	N/A
	ENSG00000303244	ENST00000793156.1		n.82+234G>A		intron	N/A
	ENSG00000303244	ENST00000793157.1		n.82+234G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17522 AN: 152050 Hom.: 2064 Cov.: 33

Gnomad AFR AF: 0.0516

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0669

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.115 AC: 17561 AN: 152170 Hom.: 2084 Cov.: 33 AF XY: 0.128 AC XY: 9522 AN XY: 74382

African (AFR) AF: 0.0516 AC: 2144 AN: 41536

American (AMR) AF: 0.339 AC: 5185 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 377 AN: 3468

East Asian (EAS) AF: 0.397 AC: 2049 AN: 5164

South Asian (SAS) AF: 0.319 AC: 1532 AN: 4806

European-Finnish (FIN) AF: 0.132 AC: 1402 AN: 10602

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0669 AC: 4551 AN: 68008

Other (OTH) AF: 0.135 AC: 285 AN: 2106

Alfa AF: 0.0875 Hom.: 3604

Bravo AF: 0.129

Asia WGS AF: 0.361 AC: 1254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.57
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs734241; hg19: chr10-115239602;