17-7281162-T-C

Variant names:

• chr17-7281162-T-C
• rs5415

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 0.752 in 152,138 control chromosomes in the GnomAD database, including 43,730 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 0.75 (43730 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 34 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 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: 0.752 AC: 114255 AN: 152020 Hom.: 43656 Cov.: 32

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.857

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.752 AC: 114393 AN: 152138 Hom.: 43730 Cov.: 32 AF XY: 0.751 AC XY: 55846 AN XY: 74364

African (AFR) AF: 0.896 AC: 37212 AN: 41528

American (AMR) AF: 0.704 AC: 10765 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2524 AN: 3468

East Asian (EAS) AF: 0.682 AC: 3512 AN: 5148

South Asian (SAS) AF: 0.696 AC: 3357 AN: 4822

European-Finnish (FIN) AF: 0.707 AC: 7481 AN: 10588

Middle Eastern (MID) AF: 0.856 AC: 250 AN: 292

European-Non Finnish (NFE) AF: 0.693 AC: 47095 AN: 67978

Other (OTH) AF: 0.765 AC: 1618 AN: 2114

Alfa AF: 0.718 Hom.: 102971

Bravo AF: 0.757

Asia WGS AF: 0.725 AC: 2523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	16
DANN	Benign	0.75
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs5415; hg19: chr17-7184481;