rs72953347

Variant names:

• chr2-178410102-G-A
• rs72953347

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 0.241 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0784

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.280

Alfa AF: 0.267 Hom.: 940

Bravo AF: 0.246

Asia WGS AF: 0.321 AC: 1118 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72953347; hg19: chr2-179274829;