chr13-23553071-G-T

Variant names:

• chr13-23553071-G-T
• rs1572072

Variant summary

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

The variant allele was found at a frequency of 0.36 in 151,794 control chromosomes in the GnomAD database, including 10,122 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 0.36 (10122 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506
• Publications: 21 publications found

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 (SAS) allele frequency at 95% confidence interval = 0.474 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

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54569 AN: 151678 Hom.: 10110 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.360 AC: 54622 AN: 151794 Hom.: 10122 Cov.: 32 AF XY: 0.360 AC XY: 26732 AN XY: 74192

African (AFR) AF: 0.286 AC: 11811 AN: 41358

American (AMR) AF: 0.349 AC: 5325 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1374 AN: 3470

East Asian (EAS) AF: 0.262 AC: 1352 AN: 5160

South Asian (SAS) AF: 0.491 AC: 2361 AN: 4810

European-Finnish (FIN) AF: 0.410 AC: 4310 AN: 10514

Middle Eastern (MID) AF: 0.369 AC: 107 AN: 290

European-Non Finnish (NFE) AF: 0.395 AC: 26822 AN: 67926

Other (OTH) AF: 0.363 AC: 766 AN: 2110

Alfa AF: 0.377 Hom.: 49107

Bravo AF: 0.347

Asia WGS AF: 0.389 AC: 1358 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	0.25
DANN	Benign	0.70
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1572072; hg19: chr13-24127210;