2-164088534-G-C

Position:

• chr2-164088534-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000429636.1(ENSG00000237844):​n.197-138275C>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,062 control chromosomes in the GnomAD database, including 2,646 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 0.17 (2646 hom., cov: 31)
• Consequence: ENST00000429636.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000429636.1	n.197-138275C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26599 AN: 151944 Hom.: 2642 Cov.: 31

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.175 AC: 26608 AN: 152062 Hom.: 2646 Cov.: 31 AF XY: 0.173 AC XY: 12875 AN XY: 74332

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.198

Alfa AF: 0.0598 Hom.: 75

Bravo AF: 0.184

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.43
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12619842; hg19: chr2-164945044;