rs72844410

chr2-85495883-T-C

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 0.177 in 152,158 control chromosomes in the GnomAD database, including 2,605 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 0.18 (2605 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26858 AN: 152040 Hom.: 2604 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0390

Gnomad SAS AF: 0.0681

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.177 AC: 26869 AN: 152158 Hom.: 2605 Cov.: 32 AF XY: 0.176 AC XY: 13067 AN XY: 74390

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.0391

Gnomad4 SAS AF: 0.0688

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.183

Alfa AF: 0.184 Hom.: 326

Bravo AF: 0.168

Asia WGS AF: 0.0650 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	9.8
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72844410; hg19: chr2-85723006;