rs2698527

Variant names:

• chr2-64272495-G-A
• rs2698527
• ENST00000717282.1:n.779+12146G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-64272495-G-A
• chr2-64272495-G-C

Variant summary

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

The ENST00000717282.1(ENSG00000288932):​n.779+12146G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 151,932 control chromosomes in the GnomAD database, including 6,443 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 0.28 (6443 hom., cov: 31)
• Consequence: ENSG00000288932 ENST00000717282.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.15
• Publications: 6 publications found

Genes affected

ENSG00000288932 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288932	ENST00000717282.1	n.779+12146G>A		intron_variant	Intron 5 of 5
ENSG00000288932	ENST00000717283.1	n.254+42855G>A		intron_variant	Intron 2 of 3
ENSG00000288932	ENST00000717284.1	n.211-18650G>A		intron_variant	Intron 2 of 2
ENSG00000288932	ENST00000717285.1	n.599+9197G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42841 AN: 151814 Hom.: 6439 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.282 AC: 42873 AN: 151932 Hom.: 6443 Cov.: 31 AF XY: 0.283 AC XY: 21025 AN XY: 74306

African (AFR) AF: 0.235 AC: 9718 AN: 41426

American (AMR) AF: 0.329 AC: 5026 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1007 AN: 3464

East Asian (EAS) AF: 0.631 AC: 3250 AN: 5152

South Asian (SAS) AF: 0.424 AC: 2043 AN: 4818

European-Finnish (FIN) AF: 0.247 AC: 2607 AN: 10550

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18340 AN: 67930

Other (OTH) AF: 0.290 AC: 610 AN: 2106

Alfa AF: 0.267 Hom.: 7436

Bravo AF: 0.288

Asia WGS AF: 0.532 AC: 1846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0020
DANN	Benign	0.50
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs2698527; hg19: chr2-64499629;