7-2904683-C-T

Variant names:

• chr7-2904683-C-T
• rs3735118

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 0.0923 in 152,110 control chromosomes in the GnomAD database, including 809 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 0.092 (809 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.01
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.202 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: 0.0923 AC: 14023 AN: 151992 Hom.: 807 Cov.: 33

Gnomad AFR AF: 0.0282

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0963

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.0719

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.0923 AC: 14033 AN: 152110 Hom.: 809 Cov.: 33 AF XY: 0.0928 AC XY: 6896 AN XY: 74346

African (AFR) AF: 0.0281 AC: 1167 AN: 41522

American (AMR) AF: 0.0963 AC: 1472 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 578 AN: 3468

East Asian (EAS) AF: 0.137 AC: 708 AN: 5150

South Asian (SAS) AF: 0.212 AC: 1023 AN: 4818

European-Finnish (FIN) AF: 0.0719 AC: 762 AN: 10596

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7982 AN: 67968

Other (OTH) AF: 0.110 AC: 230 AN: 2100

Alfa AF: 0.107 Hom.: 1229

Bravo AF: 0.0899

Asia WGS AF: 0.195 AC: 678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.20
DANN	Benign	0.37
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs3735118; hg19: chr7-2944317;