5-112513193-C-T

Variant names:

• chr5-112513193-C-T
• rs341295

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 0.361 in 152,008 control chromosomes in the GnomAD database, including 11,690 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 (11690 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 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: 0.361 AC: 54897 AN: 151890 Hom.: 11698 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.361 AC: 54884 AN: 152008 Hom.: 11690 Cov.: 32 AF XY: 0.361 AC XY: 26824 AN XY: 74260

African (AFR) AF: 0.128 AC: 5297 AN: 41482

American (AMR) AF: 0.398 AC: 6079 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1741 AN: 3468

East Asian (EAS) AF: 0.378 AC: 1949 AN: 5152

South Asian (SAS) AF: 0.359 AC: 1728 AN: 4818

European-Finnish (FIN) AF: 0.440 AC: 4632 AN: 10536

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32081 AN: 67960

Other (OTH) AF: 0.368 AC: 777 AN: 2110

Alfa AF: 0.428 Hom.: 47068

Bravo AF: 0.344

Asia WGS AF: 0.371 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.95
PhyloP100		-0.020

Splicing

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

Other links and lift over

dbSNP: rs341295; hg19: chr5-111848890; COSMIC: COSV60182722;