rs3757584

chr7-74026365-C-Achr7-74026365-C-T

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 0.123 in 152,246 control chromosomes in the GnomAD database, including 1,680 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 (1680 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.57

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18671 AN: 152128 Hom.: 1674 Cov.: 33

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0968

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0564

Gnomad OTH AF: 0.0971

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

GnomAD4 genome AF: 0.123 AC: 18697 AN: 152246 Hom.: 1680 Cov.: 33 AF XY: 0.125 AC XY: 9299 AN XY: 74446

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0274

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0968

Gnomad4 NFE AF: 0.0564

Gnomad4 OTH AF: 0.0971

Alfa AF: 0.0658 Hom.: 182

Bravo AF: 0.130

Asia WGS AF: 0.173 AC: 599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.050
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3757584; hg19: chr7-73440695;