3-70739746-C-T

Variant names:

• chr3-70739746-C-T
• rs6549354

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 0.122 in 152,002 control chromosomes in the GnomAD database, including 2,707 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 0.12 (2707 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18511 AN: 151886 Hom.: 2688 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.0649

Gnomad FIN AF: 0.0346

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0100

Gnomad OTH AF: 0.0993

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

GnomAD4 genome AF: 0.122 AC: 18574 AN: 152002 Hom.: 2707 Cov.: 32 AF XY: 0.122 AC XY: 9036 AN XY: 74288

African (AFR) AF: 0.343 AC: 14182 AN: 41390

American (AMR) AF: 0.130 AC: 1991 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3472

East Asian (EAS) AF: 0.145 AC: 750 AN: 5182

South Asian (SAS) AF: 0.0648 AC: 311 AN: 4802

European-Finnish (FIN) AF: 0.0346 AC: 366 AN: 10576

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0100 AC: 682 AN: 68002

Other (OTH) AF: 0.0983 AC: 207 AN: 2106

Alfa AF: 0.0186 Hom.: 38

Bravo AF: 0.142

Asia WGS AF: 0.129 AC: 449 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.52
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs6549354; hg19: chr3-70788897;