3-21338599-T-C

Variant names:

• chr3-21338599-T-C
• rs17548918

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 0.123 in 152,128 control chromosomes in the GnomAD database, including 1,226 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 0.12 (1226 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 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: 0.123 AC: 18732 AN: 152010 Hom.: 1226 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0609

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.123 AC: 18739 AN: 152128 Hom.: 1226 Cov.: 32 AF XY: 0.118 AC XY: 8762 AN XY: 74376

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0610

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.124

Alfa AF: 0.0833 Hom.: 157

Bravo AF: 0.121

Asia WGS AF: 0.0340 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17548918; hg19: chr3-21380091;