chr3-35954374-A-G

Variant names:

• chr3-35954374-A-G
• rs3996

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 0.462 in 152,040 control chromosomes in the GnomAD database, including 18,474 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 (18474 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.598 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: 0.463 AC: 70279 AN: 151922 Hom.: 18473 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.462 AC: 70305 AN: 152040 Hom.: 18474 Cov.: 32 AF XY: 0.462 AC XY: 34296 AN XY: 74304

African (AFR) AF: 0.207 AC: 8577 AN: 41492

American (AMR) AF: 0.415 AC: 6335 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1999 AN: 3470

East Asian (EAS) AF: 0.408 AC: 2099 AN: 5140

South Asian (SAS) AF: 0.478 AC: 2304 AN: 4820

European-Finnish (FIN) AF: 0.599 AC: 6324 AN: 10564

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.603 AC: 40987 AN: 67970

Other (OTH) AF: 0.481 AC: 1013 AN: 2104

Alfa AF: 0.519 Hom.: 5689

Bravo AF: 0.438

Asia WGS AF: 0.398 AC: 1384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.88
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs3996; hg19: chr3-35995866;