rs34193006

Variant names:

• chr2-238204382-G-A
• rs34193006

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 0.276 in 152,156 control chromosomes in the GnomAD database, including 6,205 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 0.28 (6205 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.352 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: 0.276 AC: 42007 AN: 152038 Hom.: 6200 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.276 AC: 42022 AN: 152156 Hom.: 6205 Cov.: 32 AF XY: 0.276 AC XY: 20555 AN XY: 74388

African (AFR) AF: 0.177 AC: 7366 AN: 41518

American (AMR) AF: 0.253 AC: 3870 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 735 AN: 3472

East Asian (EAS) AF: 0.210 AC: 1089 AN: 5182

South Asian (SAS) AF: 0.367 AC: 1769 AN: 4824

European-Finnish (FIN) AF: 0.334 AC: 3535 AN: 10582

Middle Eastern (MID) AF: 0.272 AC: 79 AN: 290

European-Non Finnish (NFE) AF: 0.333 AC: 22645 AN: 67988

Other (OTH) AF: 0.271 AC: 569 AN: 2098

Alfa AF: 0.310 Hom.: 957

Bravo AF: 0.266

Asia WGS AF: 0.276 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.64
DANN	Benign	0.47
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs34193006; hg19: chr2-239113023;