rs10497650

Variant names:

• chr2-184358308-A-G
• rs10497650
• ENST00000671393.1:n.550-21850A>G

Variant summary

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

The ENST00000671393.1(ENSG00000286980):​n.550-21850A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.009 in 152,144 control chromosomes in the GnomAD database, including 25 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 0.0090 (25 hom., cov: 32)
• Consequence: ENSG00000286980 ENST00000671393.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.96
• Publications: 0 publications found

Genes affected

ENSG00000286980 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0659 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671393.1. 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
	ENSG00000286980	ENST00000671393.1		n.550-21850A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00901 AC: 1369 AN: 152026 Hom.: 25 Cov.: 32

Gnomad AFR AF: 0.00545

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.00216

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.0724

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.0116

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00696

Gnomad OTH AF: 0.00720

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

GnomAD4 genome AF: 0.00900 AC: 1369 AN: 152144 Hom.: 25 Cov.: 32 AF XY: 0.00948 AC XY: 705 AN XY: 74360

African (AFR) AF: 0.00553 AC: 230 AN: 41572

American (AMR) AF: 0.00216 AC: 33 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.00115 AC: 4 AN: 3468

East Asian (EAS) AF: 0.0720 AC: 371 AN: 5156

South Asian (SAS) AF: 0.0151 AC: 73 AN: 4830

European-Finnish (FIN) AF: 0.0116 AC: 123 AN: 10570

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00696 AC: 473 AN: 67964

Other (OTH) AF: 0.00760 AC: 16 AN: 2104

Alfa AF: 0.00656 Hom.: 1

Bravo AF: 0.00867

Asia WGS AF: 0.0300 AC: 102 AN: 3412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.8
DANN	Benign	0.47
PhyloP100		2.0

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: rs10497650;

hg19: chr2-185223035;