rs1834640

Variant names:

• chr15-48099968-A-G
• rs1834640
• ENST00000730753.1:n.65-8647A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-48099968-A-G
• chr15-48099968-A-T

Variant summary

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

The ENST00000730753.1(ENSG00000295542):​n.65-8647A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,150 control chromosomes in the GnomAD database, including 16,501 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 0.29 (16501 hom., cov: 32)
• Consequence: ENSG00000295542 ENST00000730753.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.402
• Publications: 49 publications found

Genes affected

ENSG00000295542 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295542	ENST00000730753.1	n.65-8647A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44095 AN: 152032 Hom.: 16436 Cov.: 32

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.0142

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00803

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.291 AC: 44226 AN: 152150 Hom.: 16501 Cov.: 32 AF XY: 0.291 AC XY: 21684 AN XY: 74416

African (AFR) AF: 0.799 AC: 33141 AN: 41454

American (AMR) AF: 0.258 AC: 3949 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0107 AC: 37 AN: 3470

East Asian (EAS) AF: 0.903 AC: 4666 AN: 5168

South Asian (SAS) AF: 0.259 AC: 1247 AN: 4818

European-Finnish (FIN) AF: 0.0142 AC: 151 AN: 10624

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00803 AC: 546 AN: 68018

Other (OTH) AF: 0.228 AC: 483 AN: 2116

Alfa AF: 0.106 Hom.: 16911

Bravo AF: 0.336

Asia WGS AF: 0.658 AC: 2285 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.4
DANN	Benign	0.76
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs1834640; hg19: chr15-48392165;