rs7402844

chr15-75345055-C-G

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 0.657 in 152,116 control chromosomes in the GnomAD database, including 34,151 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 0.66 (34151 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.741 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: 0.657 AC: 99921 AN: 151998 Hom.: 34151 Cov.: 33

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.657 AC: 99952 AN: 152116 Hom.: 34151 Cov.: 33 AF XY: 0.658 AC XY: 48980 AN XY: 74392

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.632

Alfa AF: 0.702 Hom.: 4762

Bravo AF: 0.645

Asia WGS AF: 0.614 AC: 2139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.98
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7402844; hg19: chr15-75637396;