2-134001736-T-C

Position:

• chr2-134001736-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 0.82 in 152,210 control chromosomes in the GnomAD database, including 51,559 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 0.82 (51559 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.134001736T>C		intergenic_region
LOC105373628	XR_001739715.2	n.834-14289A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124737 AN: 152092 Hom.: 51501 Cov.: 32

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.818

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.820 AC: 124853 AN: 152210 Hom.: 51559 Cov.: 32 AF XY: 0.820 AC XY: 61026 AN XY: 74436

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.800

Gnomad4 ASJ AF: 0.764

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.779

Gnomad4 OTH AF: 0.811

Alfa AF: 0.745 Hom.: 2211

Bravo AF: 0.819

Asia WGS AF: 0.844 AC: 2937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.34
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1531957; hg19: chr2-134759307;