chr13-22719894-C-T

Variant names:

• chr13-22719894-C-T
• rs373767

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 0.356 in 151,658 control chromosomes in the GnomAD database, including 9,696 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 (9696 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 5 publications found

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 = 0.404 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: 0.356 AC: 53905 AN: 151542 Hom.: 9668 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.356 AC: 53971 AN: 151658 Hom.: 9696 Cov.: 32 AF XY: 0.352 AC XY: 26058 AN XY: 74092

African (AFR) AF: 0.409 AC: 16882 AN: 41280

American (AMR) AF: 0.360 AC: 5485 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1292 AN: 3468

East Asian (EAS) AF: 0.189 AC: 978 AN: 5164

South Asian (SAS) AF: 0.259 AC: 1247 AN: 4812

European-Finnish (FIN) AF: 0.311 AC: 3274 AN: 10514

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.347 AC: 23517 AN: 67862

Other (OTH) AF: 0.363 AC: 767 AN: 2112

Alfa AF: 0.274 Hom.: 1023

Bravo AF: 0.363

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.19
DANN	Benign	0.097
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs373767; hg19: chr13-23294033;