2-20134962-G-T

Variant names:

• chr2-20134962-G-T
• rs6531209
• ENST00000849271.1:n.140+1133C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000849271.1(ENSG00000234378):​n.140+1133C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,072 control chromosomes in the GnomAD database, including 46,911 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 0.78 (46911 hom., cov: 31)
• Consequence: ENSG00000234378 ENST00000849271.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 2 publications found

Genes affected

ENSG00000234378 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.944 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849271.1. 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
	ENSG00000234378	ENST00000849271.1		n.140+1133C>A		intron	N/A
	ENSG00000234378	ENST00000849272.1		n.249+1133C>A		intron	N/A
	ENSG00000234378	ENST00000849273.1		n.171+1133C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119112 AN: 151954 Hom.: 46859 Cov.: 31

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.784 AC: 119226 AN: 152072 Hom.: 46911 Cov.: 31 AF XY: 0.789 AC XY: 58658 AN XY: 74320

African (AFR) AF: 0.826 AC: 34265 AN: 41482

American (AMR) AF: 0.802 AC: 12262 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2537 AN: 3470

East Asian (EAS) AF: 0.966 AC: 4995 AN: 5170

South Asian (SAS) AF: 0.852 AC: 4099 AN: 4810

European-Finnish (FIN) AF: 0.776 AC: 8209 AN: 10576

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50264 AN: 67968

Other (OTH) AF: 0.781 AC: 1648 AN: 2110

Alfa AF: 0.754 Hom.: 159729

Bravo AF: 0.788

Asia WGS AF: 0.899 AC: 3123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.20
DANN	Benign	0.49
PhyloP100		-1.2

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: rs6531209;

hg19: chr2-20334723;