rs74984879

chr7-15001086-G-C

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 0.00931 in 152,162 control chromosomes in the GnomAD database, including 37 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 0.0093 (37 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.901

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0667 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: 0.00931 AC: 1416 AN: 152044 Hom.: 38 Cov.: 32

Gnomad AFR AF: 0.00193

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00380

Gnomad ASJ AF: 0.00605

Gnomad EAS AF: 0.0726

Gnomad SAS AF: 0.0560

Gnomad FIN AF: 0.0359

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00298

Gnomad OTH AF: 0.0105

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

GnomAD4 genome AF: 0.00931 AC: 1416 AN: 152162 Hom.: 37 Cov.: 32 AF XY: 0.0116 AC XY: 865 AN XY: 74382

Gnomad4 AFR AF: 0.00193

Gnomad4 AMR AF: 0.00380

Gnomad4 ASJ AF: 0.00605

Gnomad4 EAS AF: 0.0728

Gnomad4 SAS AF: 0.0556

Gnomad4 FIN AF: 0.0359

Gnomad4 NFE AF: 0.00299

Gnomad4 OTH AF: 0.0114

Alfa AF: 0.00561 Hom.: 1

Bravo AF: 0.00621

Asia WGS AF: 0.0830 AC: 287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.8
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs74984879; hg19: chr7-15040711;