rs1401223

Variant names:

• chr2-35657604-G-A
• rs1401223

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 0.455 in 152,008 control chromosomes in the GnomAD database, including 16,897 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 0.46 (16897 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 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: 0.455 AC: 69170 AN: 151890 Hom.: 16866 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.455 AC: 69237 AN: 152008 Hom.: 16897 Cov.: 32 AF XY: 0.453 AC XY: 33624 AN XY: 74296

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.435

Alfa AF: 0.437 Hom.: 1876

Bravo AF: 0.464

Asia WGS AF: 0.386 AC: 1342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.5
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: rs1401223; hg19: chr2-35882670;