rs721483

Variant names:

• chr12-43261769-T-A
• rs721483
• ENST00000756246.1:n.94+4557A>T

Variant summary

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

The ENST00000756246.1(ENSG00000298530):​n.94+4557A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 151,964 control chromosomes in the GnomAD database, including 5,515 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 0.26 (5515 hom., cov: 31)
• Consequence: ENSG00000298530 ENST00000756246.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 2 publications found

Genes affected

ENSG00000298530 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 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
ENSG00000298530	ENST00000756246.1	n.94+4557A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39929 AN: 151846 Hom.: 5518 Cov.: 31

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.263 AC: 39942 AN: 151964 Hom.: 5515 Cov.: 31 AF XY: 0.263 AC XY: 19564 AN XY: 74254

African (AFR) AF: 0.282 AC: 11688 AN: 41440

American (AMR) AF: 0.263 AC: 4014 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1020 AN: 3464

East Asian (EAS) AF: 0.551 AC: 2826 AN: 5132

South Asian (SAS) AF: 0.206 AC: 996 AN: 4826

European-Finnish (FIN) AF: 0.234 AC: 2476 AN: 10576

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16088 AN: 67964

Other (OTH) AF: 0.275 AC: 580 AN: 2110

Alfa AF: 0.247 Hom.: 591

Bravo AF: 0.267

Asia WGS AF: 0.393 AC: 1365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.013
DANN	Benign	0.44
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs721483; hg19: chr12-43655572;