rs12652757

Variant names:

• chr5-148834666-C-A
• rs12652757
• ENST00000798472.1:n.376+9369C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-148834666-C-A
• chr5-148834666-C-G
• chr5-148834666-C-T

Variant summary

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

The ENST00000798472.1(ENSG00000303969):​n.376+9369C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0709 in 152,158 control chromosomes in the GnomAD database, including 574 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 0.071 (574 hom., cov: 32)
• Consequence: ENSG00000303969 ENST00000798472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 3 publications found

Genes affected

ENSG00000303969 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 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
ENSG00000303969	ENST00000798472.1	n.376+9369C>A		intron_variant	Intron 3 of 4
ENSG00000303969	ENST00000798473.1	n.349+9369C>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.0709 AC: 10776 AN: 152040 Hom.: 574 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0392

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.0564

Gnomad SAS AF: 0.0778

Gnomad FIN AF: 0.0206

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0386

Gnomad OTH AF: 0.0624

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

GnomAD4 genome AF: 0.0709 AC: 10794 AN: 152158 Hom.: 574 Cov.: 32 AF XY: 0.0704 AC XY: 5240 AN XY: 74394

African (AFR) AF: 0.154 AC: 6407 AN: 41470

American (AMR) AF: 0.0391 AC: 598 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 112 AN: 3470

East Asian (EAS) AF: 0.0563 AC: 292 AN: 5184

South Asian (SAS) AF: 0.0782 AC: 377 AN: 4818

European-Finnish (FIN) AF: 0.0206 AC: 219 AN: 10608

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0386 AC: 2628 AN: 68012

Other (OTH) AF: 0.0627 AC: 132 AN: 2106

Alfa AF: 0.0491 Hom.: 766

Bravo AF: 0.0764

Asia WGS AF: 0.0850 AC: 295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
DANN	Benign	0.61
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs12652757; hg19: chr5-148214229;