rs3809738

Positions:

• chr17-10373329-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 0.111 in 152,120 control chromosomes in the GnomAD database, including 1,127 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 (1127 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.143 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: 0.111 AC: 16830 AN: 152002 Hom.: 1123 Cov.: 32

Gnomad AFR AF: 0.0301

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0938

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.0862

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

GnomAD4 genome AF: 0.111 AC: 16840 AN: 152120 Hom.: 1127 Cov.: 32 AF XY: 0.110 AC XY: 8193 AN XY: 74368

Gnomad4 AFR AF: 0.0300

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.0938

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.0858

Alfa AF: 0.135 Hom.: 2107

Bravo AF: 0.110

Asia WGS AF: 0.135 AC: 472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3809738; hg19: chr17-10276646;