rs1667301

Variant names:

• chr2-231559006-A-G
• rs1667301

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 0.41 in 152,058 control chromosomes in the GnomAD database, including 13,084 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 0.41 (13084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 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: 0.410 AC: 62261 AN: 151940 Hom.: 13081 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.410 AC: 62286 AN: 152058 Hom.: 13084 Cov.: 32 AF XY: 0.405 AC XY: 30098 AN XY: 74314

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.378

Alfa AF: 0.409 Hom.: 7815

Bravo AF: 0.410

Asia WGS AF: 0.209 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.3
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1667301; hg19: chr2-232423717;