chr13-57472506-A-G

Variant names:

• chr13-57472506-A-G
• rs956122
• ENST00000841145.1:n.282-14716T>C

Variant summary

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

The ENST00000841145.1(ENSG00000309440):​n.282-14716T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151,644 control chromosomes in the GnomAD database, including 8,798 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 0.33 (8798 hom., cov: 30)
• Consequence: ENSG00000309440 ENST00000841145.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 2 publications found

Genes affected

ENSG00000309440 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370217	XR_941983.1	n.577-14716T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309440	ENST00000841145.1	n.282-14716T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50406 AN: 151524 Hom.: 8769 Cov.: 30

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.333 AC: 50480 AN: 151644 Hom.: 8798 Cov.: 30 AF XY: 0.340 AC XY: 25168 AN XY: 74072

African (AFR) AF: 0.263 AC: 10903 AN: 41396

American (AMR) AF: 0.408 AC: 6188 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 805 AN: 3468

East Asian (EAS) AF: 0.521 AC: 2650 AN: 5084

South Asian (SAS) AF: 0.301 AC: 1448 AN: 4818

European-Finnish (FIN) AF: 0.437 AC: 4597 AN: 10526

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22856 AN: 67872

Other (OTH) AF: 0.292 AC: 616 AN: 2106

Alfa AF: 0.339 Hom.: 1133

Bravo AF: 0.331

Asia WGS AF: 0.419 AC: 1459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.6
DANN	Benign	0.71
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs956122; hg19: chr13-58046640;