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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124906082	XR_007088690.1	n.149+2550G>A		intron_variant	Intron 2 of 2
LOC124906082	XR_007088691.1	n.135-3134G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309294	ENST00000840148.1	n.105-3134G>A		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs707132; hg19: chr2-157214370;