rs10185424

Variant names:

• chr2-102046427-T-G
• rs10185424
• ENST00000657796.1:n.670+1724T>G

Variant summary

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

The ENST00000657796.1(ENSG00000287771):​n.670+1724T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 152,128 control chromosomes in the GnomAD database, including 29,819 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 0.62 (29819 hom., cov: 33)
• Consequence: ENSG00000287771 ENST00000657796.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 24 publications found

Genes affected

ENSG00000287771 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 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
ENSG00000287771	ENST00000657796.1	n.670+1724T>G		intron_variant	Intron 4 of 5
ENSG00000287771	ENST00000799784.1	n.163+1724T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94115 AN: 152010 Hom.: 29770 Cov.: 33

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.619 AC: 94223 AN: 152128 Hom.: 29819 Cov.: 33 AF XY: 0.627 AC XY: 46633 AN XY: 74374

African (AFR) AF: 0.734 AC: 30460 AN: 41492

American (AMR) AF: 0.629 AC: 9615 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1780 AN: 3472

East Asian (EAS) AF: 0.708 AC: 3663 AN: 5172

South Asian (SAS) AF: 0.564 AC: 2716 AN: 4818

European-Finnish (FIN) AF: 0.698 AC: 7394 AN: 10590

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36745 AN: 67972

Other (OTH) AF: 0.593 AC: 1253 AN: 2112

Alfa AF: 0.565 Hom.: 67443

Bravo AF: 0.620

Asia WGS AF: 0.652 AC: 2266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.68
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs10185424; hg19: chr2-102662888;