rs1875473

Variant names:

• chr5-154480744-C-A
• rs1875473
• ENST00000815094.1:n.233+3171C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-154480744-C-A
• chr5-154480744-C-T

Variant summary

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

The ENST00000815094.1(ENSG00000306071):​n.233+3171C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,212 control chromosomes in the GnomAD database, including 1,144 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 (1144 hom., cov: 32)
• Consequence: ENSG00000306071 ENST00000815094.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465
• Publications: 6 publications found

Genes affected

ENSG00000306071 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 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
ENSG00000306071	ENST00000815094.1	n.233+3171C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17919 AN: 152094 Hom.: 1141 Cov.: 32

Gnomad AFR AF: 0.0869

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.00769

Gnomad SAS AF: 0.0941

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.118 AC: 17939 AN: 152212 Hom.: 1144 Cov.: 32 AF XY: 0.115 AC XY: 8564 AN XY: 74410

African (AFR) AF: 0.0872 AC: 3619 AN: 41504

American (AMR) AF: 0.110 AC: 1683 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3472

East Asian (EAS) AF: 0.00771 AC: 40 AN: 5190

South Asian (SAS) AF: 0.0940 AC: 453 AN: 4820

European-Finnish (FIN) AF: 0.113 AC: 1195 AN: 10600

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10085 AN: 68012

Other (OTH) AF: 0.109 AC: 230 AN: 2108

Alfa AF: 0.125 Hom.: 1592

Bravo AF: 0.116

Asia WGS AF: 0.0590 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	4.6
DANN	Benign	0.80
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs1875473; hg19: chr5-153860304;