2-136110306-T-C

Position:

• chr2-136110306-T-C

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 0.199 in 152,234 control chromosomes in the GnomAD database, including 3,346 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 0.20 (3346 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.136110306T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30241 AN: 152116 Hom.: 3345 Cov.: 33

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.0990

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.199 AC: 30260 AN: 152234 Hom.: 3346 Cov.: 33 AF XY: 0.192 AC XY: 14274 AN XY: 74440

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.0990

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.173

Alfa AF: 0.209 Hom.: 1816

Bravo AF: 0.201

Asia WGS AF: 0.111 AC: 384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.4
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16832740; hg19: chr2-136867876;