chr2-35657517-A-G

Variant names:

• chr2-35657517-A-G
• rs1401221

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.456 in 152,030 control chromosomes in the GnomAD database, including 16,934 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 (16934 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69239 AN: 151914 Hom.: 16904 Cov.: 33

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.347

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: 0.456 AC: 69304 AN: 152030 Hom.: 16934 Cov.: 33 AF XY: 0.453 AC XY: 33663 AN XY: 74316

African (AFR) AF: 0.645 AC: 26755 AN: 41474

American (AMR) AF: 0.400 AC: 6111 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1239 AN: 3472

East Asian (EAS) AF: 0.331 AC: 1712 AN: 5176

South Asian (SAS) AF: 0.377 AC: 1813 AN: 4812

European-Finnish (FIN) AF: 0.347 AC: 3660 AN: 10542

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26527 AN: 67956

Other (OTH) AF: 0.435 AC: 918 AN: 2110

Alfa AF: 0.438 Hom.: 2636

Bravo AF: 0.465

Asia WGS AF: 0.386 AC: 1340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.7
DANN	Benign	0.38
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1401221; hg19: chr2-35882583;