rs17498319

Variant names:

• chr4-57281548-T-C
• rs17498319

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.113 in 152,186 control chromosomes in the GnomAD database, including 1,321 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 0.11 (1321 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 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: 0.113 AC: 17136 AN: 152068 Hom.: 1316 Cov.: 33

Gnomad AFR AF: 0.0288

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0988

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.0843

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.113 AC: 17133 AN: 152186 Hom.: 1321 Cov.: 33 AF XY: 0.112 AC XY: 8345 AN XY: 74402

Gnomad4 AFR AF: 0.0287

Gnomad4 AMR AF: 0.0987

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.0843

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.131

Alfa AF: 0.120 Hom.: 224

Bravo AF: 0.108

Asia WGS AF: 0.239 AC: 830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.0
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17498319; hg19: chr4-58147714;