rs3744728

Positions:

• chr17-6190631-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 0.0925 in 152,292 control chromosomes in the GnomAD database, including 849 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 0.092 (849 hom., cov: 32)
  • Exomes 𝑓: 0.033 (0 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0924 AC: 14055 AN: 152144 Hom.: 849 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.0588

Gnomad FIN AF: 0.0571

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0523

Gnomad OTH AF: 0.0826

GnomAD4 exome AF: 0.0333 AC: 1 AN: 30 Hom.: 0 AF XY: 0.0455 AC XY: 1 AN XY: 22

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0556

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0925 AC: 14084 AN: 152262 Hom.: 849 Cov.: 32 AF XY: 0.0922 AC XY: 6866 AN XY: 74430

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.0581

Gnomad4 FIN AF: 0.0571

Gnomad4 NFE AF: 0.0523

Gnomad4 OTH AF: 0.0822

Alfa AF: 0.0755 Hom.: 76

Bravo AF: 0.0979

Asia WGS AF: 0.0880 AC: 306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.6
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3744728; hg19: chr17-6093951;