7-2904683-C-T

Variant names:

• chr7-2904683-C-T
• rs3735118

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0923 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

Gnomad4 AFR AF: 0.0281

Gnomad4 AMR AF: 0.0963

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.0719

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.110

Alfa AF: 0.110 Hom.: 978

Bravo AF: 0.0899

Asia WGS AF: 0.195 AC: 678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3735118; hg19: chr7-2944317;