3-147816056-C-T

Variant names:

• chr3-147816056-C-T
• rs6785065

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 0.37 in 152,032 control chromosomes in the GnomAD database, including 11,567 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 0.37 (11567 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 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: 0.370 AC: 56187 AN: 151910 Hom.: 11542 Cov.: 33

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.370 AC: 56262 AN: 152032 Hom.: 11567 Cov.: 33 AF XY: 0.375 AC XY: 27899 AN XY: 74310

African (AFR) AF: 0.557 AC: 23098 AN: 41476

American (AMR) AF: 0.374 AC: 5710 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 912 AN: 3466

East Asian (EAS) AF: 0.470 AC: 2429 AN: 5164

South Asian (SAS) AF: 0.237 AC: 1144 AN: 4822

European-Finnish (FIN) AF: 0.428 AC: 4510 AN: 10548

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17410 AN: 67958

Other (OTH) AF: 0.345 AC: 731 AN: 2116

Alfa AF: 0.284 Hom.: 20783

Bravo AF: 0.372

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.85
DANN	Benign	0.69
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs6785065; hg19: chr3-147533843;