rs1837253

Variant names:

• chr5-111066174-T-C
• rs1837253
• ENST00000743602.1:n.29+261A>G

Variant summary

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

The ENST00000743602.1(ENSG00000296915):​n.29+261A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 152,110 control chromosomes in the GnomAD database, including 39,434 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 0.72 (39434 hom., cov: 32)
• Consequence: ENSG00000296915 ENST00000743602.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 136 publications found

Genes affected

ENSG00000296915 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.73 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
ENSG00000296915	ENST00000743602.1	n.29+261A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108974 AN: 151992 Hom.: 39407 Cov.: 32

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.717 AC: 109055 AN: 152110 Hom.: 39434 Cov.: 32 AF XY: 0.713 AC XY: 53004 AN XY: 74354

African (AFR) AF: 0.725 AC: 30090 AN: 41478

American (AMR) AF: 0.729 AC: 11144 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2570 AN: 3472

East Asian (EAS) AF: 0.379 AC: 1959 AN: 5172

South Asian (SAS) AF: 0.577 AC: 2784 AN: 4824

European-Finnish (FIN) AF: 0.759 AC: 8025 AN: 10580

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.736 AC: 50030 AN: 67992

Other (OTH) AF: 0.720 AC: 1520 AN: 2110

Alfa AF: 0.725 Hom.: 171782

Bravo AF: 0.720

Asia WGS AF: 0.515 AC: 1793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.65
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs1837253; hg19: chr5-110401872;