rs17374971

Variant names:

• chr5-23214733-T-C
• rs17374971

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 0.137 in 152,176 control chromosomes in the GnomAD database, including 1,983 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 0.14 (1983 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261
• 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 = 0.212 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: 0.137 AC: 20900 AN: 152058 Hom.: 1983 Cov.: 32

Gnomad AFR AF: 0.0378

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0754

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.137 AC: 20894 AN: 152176 Hom.: 1983 Cov.: 32 AF XY: 0.133 AC XY: 9873 AN XY: 74406

African (AFR) AF: 0.0377 AC: 1564 AN: 41538

American (AMR) AF: 0.122 AC: 1870 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 386 AN: 3466

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5180

South Asian (SAS) AF: 0.0759 AC: 366 AN: 4824

European-Finnish (FIN) AF: 0.155 AC: 1640 AN: 10576

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14604 AN: 67998

Other (OTH) AF: 0.124 AC: 261 AN: 2106

Alfa AF: 0.176 Hom.: 349

Bravo AF: 0.130

Asia WGS AF: 0.0320 AC: 114 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	1.8
DANN	Benign	0.30
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs17374971; hg19: chr5-23214842;