rs2486866

Variant names:

• chr10-6971254-C-T
• rs2486866
• ENST00000652889.2:n.123+16351G>A

Variant summary

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

The ENST00000652889.2(ENSG00000287277):​n.123+16351G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 152,054 control chromosomes in the GnomAD database, including 25,942 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 0.58 (25942 hom., cov: 32)
• Consequence: ENSG00000287277 ENST00000652889.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633
• Publications: 1 publications found

Genes affected

ENSG00000287277 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376387	NR_188183.1	n.273-35846G>A		intron_variant	Intron 2 of 4
LOC105376387	NR_188184.1	n.74+16351G>A		intron_variant	Intron 1 of 4
LOC105376387	NR_188185.1	n.74+16351G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287277	ENST00000652889.2	n.123+16351G>A		intron_variant	Intron 1 of 3
ENSG00000287277	ENST00000654037.2	n.198+15282G>A		intron_variant	Intron 2 of 5
ENSG00000287277	ENST00000654694.1	n.80+16351G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88105 AN: 151936 Hom.: 25935 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.580 AC: 88150 AN: 152054 Hom.: 25942 Cov.: 32 AF XY: 0.572 AC XY: 42465 AN XY: 74296

African (AFR) AF: 0.574 AC: 23824 AN: 41492

American (AMR) AF: 0.498 AC: 7609 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2464 AN: 3472

East Asian (EAS) AF: 0.394 AC: 2031 AN: 5158

South Asian (SAS) AF: 0.506 AC: 2438 AN: 4816

European-Finnish (FIN) AF: 0.509 AC: 5382 AN: 10580

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42401 AN: 67950

Other (OTH) AF: 0.606 AC: 1280 AN: 2112

Alfa AF: 0.575 Hom.: 4144

Bravo AF: 0.578

Asia WGS AF: 0.400 AC: 1393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.98
DANN	Benign	0.52
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2486866; hg19: chr10-7013216;