3-1669864-C-T

Variant names:

• chr3-1669864-C-T
• rs3856831

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 0.151 in 152,124 control chromosomes in the GnomAD database, including 2,259 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 0.15 (2259 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.248 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: 0.151 AC: 22886 AN: 152006 Hom.: 2246 Cov.: 32

Gnomad AFR AF: 0.0437

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.0871

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.151 AC: 22914 AN: 152124 Hom.: 2259 Cov.: 32 AF XY: 0.156 AC XY: 11625 AN XY: 74360

African (AFR) AF: 0.0438 AC: 1819 AN: 41544

American (AMR) AF: 0.254 AC: 3878 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0871 AC: 302 AN: 3466

East Asian (EAS) AF: 0.137 AC: 708 AN: 5170

South Asian (SAS) AF: 0.153 AC: 738 AN: 4820

European-Finnish (FIN) AF: 0.255 AC: 2696 AN: 10576

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12374 AN: 67976

Other (OTH) AF: 0.143 AC: 301 AN: 2112

Alfa AF: 0.152 Hom.: 778

Bravo AF: 0.145

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.021
DANN	Benign	0.28
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs3856831; hg19: chr3-1711548;