rs6742722

Variant names:

• chr2-236132153-G-A
• rs6742722

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;