2-164038051-T-C

Variant names:

• chr2-164038051-T-C
• rs12692709
• ENST00000429636.1:n.197-87792A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000429636.1(ENSG00000237844):​n.197-87792A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000237844 ENST00000429636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.519
• Publications: 5 publications found

Genes affected

ENSG00000237844 (HGNC:58942):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429636.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000237844	ENST00000429636.1	TSL:3	n.197-87792A>G		intron	N/A

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

African (AFR) AF: 0.827 AC: 34325 AN: 41498

American (AMR) AF: 0.619 AC: 9448 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1855 AN: 3470

East Asian (EAS) AF: 0.500 AC: 2583 AN: 5162

South Asian (SAS) AF: 0.602 AC: 2900 AN: 4818

European-Finnish (FIN) AF: 0.482 AC: 5077 AN: 10532

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35245 AN: 67960

Other (OTH) AF: 0.596 AC: 1259 AN: 2114

Alfa AF: 0.550 Hom.: 32531

Bravo AF: 0.636

Asia WGS AF: 0.563 AC: 1961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	16
DANN	Benign	0.77
PhyloP100		0.52

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12692709;

hg19: chr2-164894561;