rs1395993

Variant names:

• chr3-21328094-T-C
• rs1395993

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 0.461 in 151,864 control chromosomes in the GnomAD database, including 18,243 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 0.46 (18243 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 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: 0.461 AC: 69914 AN: 151748 Hom.: 18217 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.461 AC: 70002 AN: 151864 Hom.: 18243 Cov.: 32 AF XY: 0.472 AC XY: 35037 AN XY: 74228

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.860

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.440

Alfa AF: 0.353 Hom.: 12434

Bravo AF: 0.482

Asia WGS AF: 0.756 AC: 2623 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.083
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1395993; hg19: chr3-21369586;