rs17011370

Variant names:

• chr2-75465497-C-T
• rs17011370

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 0.0644 in 152,244 control chromosomes in the GnomAD database, including 438 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 0.064 (438 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.123 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: 0.0644 AC: 9798 AN: 152126 Hom.: 438 Cov.: 32

Gnomad AFR AF: 0.0438

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0447

Gnomad EAS AF: 0.0966

Gnomad SAS AF: 0.0984

Gnomad FIN AF: 0.0251

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0626

Gnomad OTH AF: 0.0752

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

GnomAD4 genome AF: 0.0644 AC: 9803 AN: 152244 Hom.: 438 Cov.: 32 AF XY: 0.0644 AC XY: 4792 AN XY: 74422

African (AFR) AF: 0.0437 AC: 1817 AN: 41564

American (AMR) AF: 0.128 AC: 1950 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0447 AC: 155 AN: 3470

East Asian (EAS) AF: 0.0964 AC: 499 AN: 5176

South Asian (SAS) AF: 0.0989 AC: 477 AN: 4822

European-Finnish (FIN) AF: 0.0251 AC: 266 AN: 10604

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0626 AC: 4258 AN: 68004

Other (OTH) AF: 0.0754 AC: 159 AN: 2110

Alfa AF: 0.0648 Hom.: 103

Bravo AF: 0.0707

Asia WGS AF: 0.101 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.35
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs17011370; hg19: chr2-75692623;