rs72953347

Variant names:

• chr2-178410102-G-A
• rs72953347

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 0.241 in 151,928 control chromosomes in the GnomAD database, including 5,351 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 0.24 (5351 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.64
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36695 AN: 151810 Hom.: 5355 Cov.: 32

Gnomad AFR AF: 0.0785

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.241 AC: 36687 AN: 151928 Hom.: 5351 Cov.: 32 AF XY: 0.246 AC XY: 18262 AN XY: 74258

African (AFR) AF: 0.0784 AC: 3250 AN: 41452

American (AMR) AF: 0.349 AC: 5331 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1473 AN: 3466

East Asian (EAS) AF: 0.438 AC: 2263 AN: 5172

South Asian (SAS) AF: 0.252 AC: 1216 AN: 4816

European-Finnish (FIN) AF: 0.287 AC: 3020 AN: 10506

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19178 AN: 67938

Other (OTH) AF: 0.280 AC: 590 AN: 2104

Alfa AF: 0.268 Hom.: 2050

Bravo AF: 0.246

Asia WGS AF: 0.321 AC: 1118 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.9
DANN	Benign	0.65
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs72953347; hg19: chr2-179274829;