rs17498319

Positions:

• chr4-57281548-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;