rs10506466

Variant names:

• chr12-63755759-A-G
• rs10506466
• ENST00000509615.2:n.238+39722T>C

Variant summary

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

The ENST00000509615.2(ENSG00000249753):​n.238+39722T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,154 control chromosomes in the GnomAD database, including 1,371 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 0.12 (1371 hom., cov: 32)
• Consequence: ENSG00000249753 ENST00000509615.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 1 publications found

Genes affected

ENSG00000249753 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 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
ENSG00000249753	ENST00000509615.2	n.238+39722T>C		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17707 AN: 152036 Hom.: 1367 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0802

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0826

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0756

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.117 AC: 17733 AN: 152154 Hom.: 1371 Cov.: 32 AF XY: 0.117 AC XY: 8708 AN XY: 74390

African (AFR) AF: 0.152 AC: 6306 AN: 41492

American (AMR) AF: 0.144 AC: 2199 AN: 15284

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

East Asian (EAS) AF: 0.375 AC: 1942 AN: 5174

South Asian (SAS) AF: 0.132 AC: 635 AN: 4814

European-Finnish (FIN) AF: 0.0826 AC: 875 AN: 10590

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0756 AC: 5140 AN: 68012

Other (OTH) AF: 0.125 AC: 264 AN: 2116

Alfa AF: 0.105 Hom.: 450

Bravo AF: 0.123

Asia WGS AF: 0.265 AC: 920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.24
DANN	Benign	0.22
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10506466; hg19: chr12-64149539;