rs1656404

Positions:

• chr2-232515231-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 0.175 in 151,968 control chromosomes in the GnomAD database, including 2,466 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 (2466 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.159

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26590 AN: 151848 Hom.: 2464 Cov.: 31

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0249

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.175 AC: 26595 AN: 151968 Hom.: 2466 Cov.: 31 AF XY: 0.172 AC XY: 12750 AN XY: 74280

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0251

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.184

Alfa AF: 0.175 Hom.: 921

Bravo AF: 0.175

Asia WGS AF: 0.103 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1656404; hg19: chr2-233379941;