chr2-164038051-T-C

Position:

• chr2-164038051-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.614 in 152,016 control chromosomes in the GnomAD database, including 30,169 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 0.61 (30169 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.519

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.164038051T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000237844	ENST00000429636.1	n.197-87792A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93274 AN: 151898 Hom.: 30106 Cov.: 31

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.614 AC: 93396 AN: 152016 Hom.: 30169 Cov.: 31 AF XY: 0.610 AC XY: 45285 AN XY: 74286

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.596

Alfa AF: 0.529 Hom.: 19774

Bravo AF: 0.636

Asia WGS AF: 0.563 AC: 1961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	16
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12692709; hg19: chr2-164894561;