2-138964859-G-C

Variant names:

• chr2-138964859-G-C
• rs1872387
• ENST00000656547.2:n.208-9783G>C

Variant summary

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

The ENST00000656547.2(ENSG00000287147):​n.208-9783G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 151,922 control chromosomes in the GnomAD database, including 22,872 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 0.55 (22872 hom., cov: 31)
• Consequence: ENSG00000287147 ENST00000656547.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 2 publications found

Genes affected

ENSG00000287147 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656547.2. 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
	ENSG00000287147	ENST00000656547.2		n.208-9783G>C		intron	N/A
	ENSG00000287147	ENST00000821872.1		n.165-3891G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.547 AC: 82993 AN: 151804 Hom.: 22851 Cov.: 31

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.547 AC: 83059 AN: 151922 Hom.: 22872 Cov.: 31 AF XY: 0.542 AC XY: 40257 AN XY: 74246

African (AFR) AF: 0.560 AC: 23184 AN: 41390

American (AMR) AF: 0.511 AC: 7798 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1806 AN: 3472

East Asian (EAS) AF: 0.385 AC: 1984 AN: 5154

South Asian (SAS) AF: 0.489 AC: 2359 AN: 4820

European-Finnish (FIN) AF: 0.589 AC: 6219 AN: 10564

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37929 AN: 67950

Other (OTH) AF: 0.528 AC: 1113 AN: 2108

Alfa AF: 0.467 Hom.: 1434

Bravo AF: 0.542

Asia WGS AF: 0.472 AC: 1641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.55
DANN	Benign	0.67
PhyloP100		-1.7

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: rs1872387;

hg19: chr2-139722429;