2-238205153-T-C

Variant names:

• chr2-238205153-T-C
• rs11695186

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.849

Gnomad4 EAS AF: 0.959

Gnomad4 SAS AF: 0.792

Gnomad4 FIN AF: 0.762

Gnomad4 NFE AF: 0.779

Gnomad4 OTH AF: 0.819

Alfa AF: 0.787 Hom.: 54184

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11695186; hg19: chr2-239113794;