3-35940638-C-T

Variant names:

• chr3-35940638-C-T
• rs6799705

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 0.0718 in 152,126 control chromosomes in the GnomAD database, including 526 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 0.072 (526 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.131 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: 0.0718 AC: 10907 AN: 152008 Hom.: 523 Cov.: 33

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0419

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0389

Gnomad FIN AF: 0.0319

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0531

Gnomad OTH AF: 0.0649

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

GnomAD4 genome AF: 0.0718 AC: 10922 AN: 152126 Hom.: 526 Cov.: 33 AF XY: 0.0686 AC XY: 5103 AN XY: 74372

African (AFR) AF: 0.134 AC: 5535 AN: 41456

American (AMR) AF: 0.0420 AC: 641 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.0385 AC: 186 AN: 4826

European-Finnish (FIN) AF: 0.0319 AC: 338 AN: 10588

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0531 AC: 3611 AN: 68002

Other (OTH) AF: 0.0643 AC: 136 AN: 2116

Alfa AF: 0.0596 Hom.: 1381

Bravo AF: 0.0755

Asia WGS AF: 0.0290 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.77
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs6799705; hg19: chr3-35982130;