rs1390796

Variant names:

• chr3-162659339-T-C
• rs1390796

Your query was ambiguous. Multiple possible variants found:

• chr3-162659339-T-C
• chr3-162659339-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0672 in 152,220 control chromosomes in the GnomAD database, including 864 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 0.067 (864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0670 AC: 10192 AN: 152102 Hom.: 851 Cov.: 32

Gnomad AFR AF: 0.0438

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0907

Gnomad ASJ AF: 0.0856

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0590

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0404

Gnomad OTH AF: 0.0608

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

GnomAD4 genome AF: 0.0672 AC: 10224 AN: 152220 Hom.: 864 Cov.: 32 AF XY: 0.0720 AC XY: 5359 AN XY: 74424

African (AFR) AF: 0.0440 AC: 1829 AN: 41562

American (AMR) AF: 0.0906 AC: 1385 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0856 AC: 297 AN: 3470

East Asian (EAS) AF: 0.467 AC: 2402 AN: 5144

South Asian (SAS) AF: 0.138 AC: 666 AN: 4824

European-Finnish (FIN) AF: 0.0590 AC: 627 AN: 10622

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0404 AC: 2748 AN: 68000

Other (OTH) AF: 0.0724 AC: 153 AN: 2112

Alfa AF: 0.0481 Hom.: 37

Bravo AF: 0.0687

Asia WGS AF: 0.313 AC: 1087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.86
DANN	Benign	0.53
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs1390796; hg19: chr3-162377127;