rs7402844

Variant names:

• chr15-75345055-C-G
• rs7402844

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.467 AC: 19370 AN: 41440

American (AMR) AF: 0.704 AC: 10757 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2138 AN: 3470

East Asian (EAS) AF: 0.650 AC: 3366 AN: 5178

South Asian (SAS) AF: 0.611 AC: 2949 AN: 4826

European-Finnish (FIN) AF: 0.803 AC: 8511 AN: 10600

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50769 AN: 68000

Other (OTH) AF: 0.632 AC: 1336 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.98
DANN	Benign	0.30
PhyloP100		0.023

Splicing

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

Other links and lift over

dbSNP: rs7402844; hg19: chr15-75637396;