rs6742722

chr2-236132153-G-A

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 0.286 in 152,020 control chromosomes in the GnomAD database, including 10,996 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 0.29 (10996 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 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: 0.286 AC: 43436 AN: 151902 Hom.: 10969 Cov.: 32

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0279

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.286 AC: 43508 AN: 152020 Hom.: 10996 Cov.: 32 AF XY: 0.280 AC XY: 20810 AN XY: 74332

Gnomad4 AFR AF: 0.689

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.0282

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.252

Alfa AF: 0.153 Hom.: 3433

Bravo AF: 0.301

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.0060
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6742722; hg19: chr2-237040797;