chr7-74026365-C-A

Variant names:

• chr7-74026365-C-A
• rs3757584

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;