rs74984879

Variant names:

• chr7-15001086-G-C
• rs74984879

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;