3-25697750-T-C

Variant names:

• chr3-25697750-T-C
• rs6785846

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 0.652 in 152,162 control chromosomes in the GnomAD database, including 38,018 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 0.65 (38018 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.676
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 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: 0.653 AC: 99221 AN: 152044 Hom.: 38013 Cov.: 33

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.652 AC: 99242 AN: 152162 Hom.: 38018 Cov.: 33 AF XY: 0.656 AC XY: 48784 AN XY: 74394

African (AFR) AF: 0.218 AC: 9038 AN: 41504

American (AMR) AF: 0.726 AC: 11095 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2920 AN: 3466

East Asian (EAS) AF: 0.878 AC: 4549 AN: 5182

South Asian (SAS) AF: 0.770 AC: 3712 AN: 4818

European-Finnish (FIN) AF: 0.794 AC: 8424 AN: 10604

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57050 AN: 67998

Other (OTH) AF: 0.704 AC: 1486 AN: 2110

Alfa AF: 0.773 Hom.: 56147

Bravo AF: 0.629

Asia WGS AF: 0.762 AC: 2645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	15
DANN	Benign	0.65
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs6785846; hg19: chr3-25739241;