2-136035544-T-C

Variant names:

• chr2-136035544-T-C
• rs4954555

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 0.189 in 152,088 control chromosomes in the GnomAD database, including 4,327 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 0.19 (4327 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.589

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 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: 0.189 AC: 28739 AN: 151970 Hom.: 4313 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.0625

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.189 AC: 28792 AN: 152088 Hom.: 4327 Cov.: 32 AF XY: 0.195 AC XY: 14494 AN XY: 74360

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.0626

Gnomad4 OTH AF: 0.202

Alfa AF: 0.0921 Hom.: 1626

Bravo AF: 0.207

Asia WGS AF: 0.337 AC: 1172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.61
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4954555; hg19: chr2-136793114;