rs34272954

Variant names:

• chr2-238204869-A-C
• rs34272954

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 152,158 control chromosomes in the GnomAD database, including 6,216 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 (6216 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.353 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: 0.277 AC: 42044 AN: 152040 Hom.: 6211 Cov.: 33

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: 0.367

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.271

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: 42059 AN: 152158 Hom.: 6216 Cov.: 33 AF XY: 0.277 AC XY: 20568 AN XY: 74384

African (AFR) AF: 0.177 AC: 7367 AN: 41508

American (AMR) AF: 0.254 AC: 3878 AN: 15286

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

East Asian (EAS) AF: 0.210 AC: 1085 AN: 5174

South Asian (SAS) AF: 0.367 AC: 1771 AN: 4822

European-Finnish (FIN) AF: 0.334 AC: 3536 AN: 10576

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.333 AC: 22669 AN: 68006

Other (OTH) AF: 0.272 AC: 573 AN: 2110

Alfa AF: 0.310 Hom.: 957

Bravo AF: 0.266

Asia WGS AF: 0.276 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.80
DANN	Benign	0.60
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs34272954; hg19: chr2-239113510;