2-238205153-T-C

Variant names:

• chr2-238205153-T-C
• rs11695186

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 0.803 in 152,064 control chromosomes in the GnomAD database, including 49,210 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 0.80 (49210 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.936 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: 0.803 AC: 122062 AN: 151946 Hom.: 49163 Cov.: 31

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.803 AC: 122168 AN: 152064 Hom.: 49210 Cov.: 31 AF XY: 0.805 AC XY: 59826 AN XY: 74326

African (AFR) AF: 0.821 AC: 34048 AN: 41468

American (AMR) AF: 0.831 AC: 12692 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2945 AN: 3470

East Asian (EAS) AF: 0.959 AC: 4958 AN: 5172

South Asian (SAS) AF: 0.792 AC: 3824 AN: 4826

European-Finnish (FIN) AF: 0.762 AC: 8036 AN: 10550

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.779 AC: 52964 AN: 67988

Other (OTH) AF: 0.819 AC: 1729 AN: 2110

Alfa AF: 0.790 Hom.: 152164

Bravo AF: 0.808

Asia WGS AF: 0.848 AC: 2947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.26
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11695186; hg19: chr2-239113794;