2-240352405-G-A

Variant names:

• chr2-240352405-G-A
• rs10933595

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 0.503 in 152,074 control chromosomes in the GnomAD database, including 20,237 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 0.50 (20237 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76449 AN: 151956 Hom.: 20237 Cov.: 34

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.503 AC: 76481 AN: 152074 Hom.: 20237 Cov.: 34 AF XY: 0.497 AC XY: 36937 AN XY: 74320

African (AFR) AF: 0.346 AC: 14373 AN: 41482

American (AMR) AF: 0.536 AC: 8188 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2138 AN: 3470

East Asian (EAS) AF: 0.384 AC: 1976 AN: 5150

South Asian (SAS) AF: 0.369 AC: 1780 AN: 4818

European-Finnish (FIN) AF: 0.526 AC: 5555 AN: 10562

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40599 AN: 67986

Other (OTH) AF: 0.545 AC: 1153 AN: 2116

Alfa AF: 0.570 Hom.: 41895

Bravo AF: 0.498

Asia WGS AF: 0.365 AC: 1267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.13
DANN	Benign	0.63
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10933595; hg19: chr2-241291822;