5-23243916-C-T

Variant names:

• chr5-23243916-C-T
• rs17376026

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 0.239 in 152,036 control chromosomes in the GnomAD database, including 5,732 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 0.24 (5732 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526
• 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 = 0.348 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: 0.239 AC: 36379 AN: 151918 Hom.: 5730 Cov.: 33

Gnomad AFR AF: 0.0702

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.00463

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.239 AC: 36376 AN: 152036 Hom.: 5732 Cov.: 33 AF XY: 0.236 AC XY: 17554 AN XY: 74308

African (AFR) AF: 0.0700 AC: 2904 AN: 41494

American (AMR) AF: 0.216 AC: 3302 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1121 AN: 3468

East Asian (EAS) AF: 0.00464 AC: 24 AN: 5174

South Asian (SAS) AF: 0.174 AC: 840 AN: 4818

European-Finnish (FIN) AF: 0.315 AC: 3320 AN: 10534

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23889 AN: 67960

Other (OTH) AF: 0.252 AC: 533 AN: 2112

Alfa AF: 0.305 Hom.: 21563

Bravo AF: 0.226

Asia WGS AF: 0.0750 AC: 264 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.44
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs17376026; hg19: chr5-23244025;