rs12653736

Variant names:

• chr5-111064929-G-T
• rs12653736
• ENST00000743602.1:n.29+1506C>A

Variant summary

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

The ENST00000743602.1(ENSG00000296915):​n.29+1506C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0409 in 152,194 control chromosomes in the GnomAD database, including 188 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 0.041 (188 hom., cov: 33)
• Consequence: ENSG00000296915 ENST00000743602.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.897
• Publications: 1 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 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+1506C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0408 AC: 6211 AN: 152076 Hom.: 186 Cov.: 33

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0272

Gnomad ASJ AF: 0.0357

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0756

Gnomad FIN AF: 0.0326

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0274

Gnomad OTH AF: 0.0532

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

GnomAD4 genome AF: 0.0409 AC: 6227 AN: 152194 Hom.: 188 Cov.: 33 AF XY: 0.0415 AC XY: 3090 AN XY: 74388

African (AFR) AF: 0.0537 AC: 2228 AN: 41518

American (AMR) AF: 0.0271 AC: 414 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0357 AC: 124 AN: 3470

East Asian (EAS) AF: 0.142 AC: 734 AN: 5164

South Asian (SAS) AF: 0.0752 AC: 363 AN: 4824

European-Finnish (FIN) AF: 0.0326 AC: 345 AN: 10598

Middle Eastern (MID) AF: 0.0514 AC: 15 AN: 292

European-Non Finnish (NFE) AF: 0.0274 AC: 1865 AN: 68026

Other (OTH) AF: 0.0546 AC: 115 AN: 2108

Alfa AF: 0.0324 Hom.: 143

Bravo AF: 0.0384

Asia WGS AF: 0.123 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.56
DANN	Benign	0.80
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs12653736; hg19: chr5-110400627;