rs10496600

Variant names:

• chr2-122801711-A-C
• rs10496600
• ENST00000657880.2:n.825-22043A>C

Variant summary

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

The ENST00000657880.2(ENSG00000286481):​n.825-22043A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0193 in 152,226 control chromosomes in the GnomAD database, including 46 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 0.019 (46 hom., cov: 32)
• Consequence: ENSG00000286481 ENST00000657880.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 0 publications found

Genes affected

ENSG00000286481 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373594	XR_923288.1	n.1553-214T>G		intron_variant	Intron 3 of 3
LOC105373594	XR_923289.3	n.1553-1495T>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286481	ENST00000657880.2	n.825-22043A>C		intron_variant	Intron 4 of 8
ENSG00000286481	ENST00000687364.1	n.84-22043A>C		intron_variant	Intron 1 of 5
ENSG00000286481	ENST00000770504.1	n.365-22043A>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0192 AC: 2925 AN: 152108 Hom.: 48 Cov.: 32

Gnomad AFR AF: 0.0438

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0107

Gnomad ASJ AF: 0.0802

Gnomad EAS AF: 0.00367

Gnomad SAS AF: 0.0737

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00350

Gnomad OTH AF: 0.0196

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

GnomAD4 genome AF: 0.0193 AC: 2941 AN: 152226 Hom.: 46 Cov.: 32 AF XY: 0.0200 AC XY: 1486 AN XY: 74434

African (AFR) AF: 0.0441 AC: 1831 AN: 41536

American (AMR) AF: 0.0107 AC: 164 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0802 AC: 278 AN: 3468

East Asian (EAS) AF: 0.00387 AC: 20 AN: 5172

South Asian (SAS) AF: 0.0734 AC: 354 AN: 4824

European-Finnish (FIN) AF: 0.0000942 AC: 1 AN: 10620

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00350 AC: 238 AN: 68000

Other (OTH) AF: 0.0198 AC: 42 AN: 2116

Alfa AF: 0.0168 Hom.: 3

Bravo AF: 0.0188

Asia WGS AF: 0.0480 AC: 166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.045
DANN	Benign	0.39
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs10496600; hg19: chr2-123559287;