3-143935035-C-T

Variant names:

• chr3-143935035-C-T
• rs765695

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 0.557 in 152,010 control chromosomes in the GnomAD database, including 25,733 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 0.56 (25733 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84622 AN: 151890 Hom.: 25690 Cov.: 32

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.557 AC: 84725 AN: 152010 Hom.: 25733 Cov.: 32 AF XY: 0.558 AC XY: 41495 AN XY: 74304

African (AFR) AF: 0.816 AC: 33894 AN: 41522

American (AMR) AF: 0.513 AC: 7822 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1488 AN: 3466

East Asian (EAS) AF: 0.543 AC: 2809 AN: 5176

South Asian (SAS) AF: 0.486 AC: 2342 AN: 4818

European-Finnish (FIN) AF: 0.464 AC: 4897 AN: 10550

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.439 AC: 29831 AN: 67926

Other (OTH) AF: 0.534 AC: 1126 AN: 2110

Alfa AF: 0.411 Hom.: 1805

Bravo AF: 0.568

Asia WGS AF: 0.543 AC: 1889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.78
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs765695; hg19: chr3-143653877;