chr12-71039513-C-T

Variant names:

• chr12-71039513-C-T
• rs7955901
• ENST00000716229.1:n.418-5265G>A

Variant summary

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

The ENST00000716229.1(ENSG00000258053):​n.418-5265G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 151,988 control chromosomes in the GnomAD database, including 28,068 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 0.60 (28068 hom., cov: 31)
• Consequence: ENSG00000258053 ENST00000716229.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664
• Publications: 42 publications found

Genes affected

ENSG00000258053 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 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
ENSG00000258053	ENST00000716229.1	n.418-5265G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90573 AN: 151870 Hom.: 28023 Cov.: 31

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.597 AC: 90673 AN: 151988 Hom.: 28068 Cov.: 31 AF XY: 0.595 AC XY: 44184 AN XY: 74274

African (AFR) AF: 0.750 AC: 31085 AN: 41442

American (AMR) AF: 0.482 AC: 7361 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1498 AN: 3472

East Asian (EAS) AF: 0.341 AC: 1759 AN: 5152

South Asian (SAS) AF: 0.576 AC: 2777 AN: 4818

European-Finnish (FIN) AF: 0.654 AC: 6910 AN: 10572

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37592 AN: 67944

Other (OTH) AF: 0.534 AC: 1124 AN: 2106

Alfa AF: 0.565 Hom.: 12541

Bravo AF: 0.586

Asia WGS AF: 0.446 AC: 1556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.72
DANN	Benign	0.40
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs7955901; hg19: chr12-71433293;