rs12530731

Variant names:

• chr7-73944846-G-A
• rs12530731
• ENST00000728270.1:n.275+27920G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-73944846-G-A
• chr7-73944846-G-T

Variant summary

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

The ENST00000728270.1(ENSG00000261467):​n.275+27920G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 151,946 control chromosomes in the GnomAD database, including 8,680 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 0.30 (8680 hom., cov: 32)
• Consequence: ENSG00000261467 ENST00000728270.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995
• Publications: 5 publications found

Genes affected

ENSG00000261467 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.493 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
ENSG00000261467	ENST00000728270.1	n.275+27920G>A		intron_variant	Intron 1 of 1
ENSG00000261467	ENST00000728271.1	n.229+2507G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46235 AN: 151830 Hom.: 8640 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.305 AC: 46331 AN: 151946 Hom.: 8680 Cov.: 32 AF XY: 0.311 AC XY: 23102 AN XY: 74272

African (AFR) AF: 0.497 AC: 20593 AN: 41398

American (AMR) AF: 0.335 AC: 5120 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 681 AN: 3466

East Asian (EAS) AF: 0.510 AC: 2633 AN: 5166

South Asian (SAS) AF: 0.453 AC: 2183 AN: 4816

European-Finnish (FIN) AF: 0.180 AC: 1900 AN: 10544

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12391 AN: 67966

Other (OTH) AF: 0.269 AC: 566 AN: 2106

Alfa AF: 0.242 Hom.: 5429

Bravo AF: 0.321

Asia WGS AF: 0.465 AC: 1616 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.45
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs12530731; hg19: chr7-73359176;