rs707132

Variant names:

• chr2-156357858-G-A
• rs707132
• ENST00000840148.1:n.105-3134G>A

Variant summary

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

The ENST00000840148.1(ENSG00000309294):​n.105-3134G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 152,036 control chromosomes in the GnomAD database, including 13,966 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 0.39 (13966 hom., cov: 33)
• Consequence: ENSG00000309294 ENST00000840148.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200
• Publications: 5 publications found

Genes affected

ENSG00000309294 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000840148.1. 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
	ENSG00000309294	ENST00000840148.1		n.105-3134G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59554 AN: 151918 Hom.: 13964 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.392 AC: 59552 AN: 152036 Hom.: 13966 Cov.: 33 AF XY: 0.388 AC XY: 28831 AN XY: 74310

African (AFR) AF: 0.151 AC: 6256 AN: 41476

American (AMR) AF: 0.313 AC: 4772 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1649 AN: 3472

East Asian (EAS) AF: 0.195 AC: 1011 AN: 5178

South Asian (SAS) AF: 0.429 AC: 2066 AN: 4814

European-Finnish (FIN) AF: 0.555 AC: 5847 AN: 10532

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.538 AC: 36549 AN: 67976

Other (OTH) AF: 0.394 AC: 832 AN: 2114

Alfa AF: 0.482 Hom.: 48838

Bravo AF: 0.356

Asia WGS AF: 0.297 AC: 1032 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	5.8
DANN	Benign	0.44
PhyloP100		-0.020

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: rs707132;

hg19: chr2-157214370;