10-86752585-G-C

Variant names:

• chr10-86752585-G-C
• rs12248786
• ENST00000608826.2:n.3802C>G

Variant summary

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

The ENST00000608826.2(ENSG00000272631):​n.3802C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,450 control chromosomes in the GnomAD database, including 1,859 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 0.14 (1856 hom., cov: 31)
  • Exomes 𝑓: 0.10 (3 hom.)
• Consequence: ENSG00000272631 ENST00000608826.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386
• Publications: 1 publications found

Genes affected

ENSG00000272631 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 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
ENSG00000272631	ENST00000608826.2	n.3802C>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000272631	ENST00000740897.1	n.526+3166C>G		intron_variant	Intron 1 of 1
ENSG00000272631	ENST00000740898.1	n.230+3456C>G		intron_variant	Intron 1 of 1
ENSG00000272631	ENST00000740899.1	n.201+3166C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20697 AN: 151852 Hom.: 1847 Cov.: 31

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.0783

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.0239

Gnomad SAS AF: 0.0711

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0930

Gnomad OTH AF: 0.126

GnomAD4 exome AF: 0.104 AC: 50 AN: 480 Hom.: 3 Cov.: 0 AF XY: 0.115 AC XY: 41 AN XY: 356

African (AFR) AF: 0.250 AC: 3 AN: 12

American (AMR) AF: 0.00 AC: 0 AN: 6

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AF: 0.00 AC: 0 AN: 16

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.0500 AC: 1 AN: 20

Middle Eastern (MID) AF: 0.333 AC: 2 AN: 6

European-Non Finnish (NFE) AF: 0.103 AC: 40 AN: 390

Other (OTH) AF: 0.125 AC: 3 AN: 24

GnomAD4 genome AF: 0.136 AC: 20736 AN: 151970 Hom.: 1856 Cov.: 31 AF XY: 0.136 AC XY: 10074 AN XY: 74284

African (AFR) AF: 0.253 AC: 10467 AN: 41388

American (AMR) AF: 0.0781 AC: 1192 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 348 AN: 3466

East Asian (EAS) AF: 0.0234 AC: 121 AN: 5180

South Asian (SAS) AF: 0.0713 AC: 343 AN: 4808

European-Finnish (FIN) AF: 0.141 AC: 1492 AN: 10568

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0930 AC: 6320 AN: 67986

Other (OTH) AF: 0.130 AC: 274 AN: 2112

Alfa AF: 0.106 Hom.: 140

Bravo AF: 0.139

Asia WGS AF: 0.0850 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.2
DANN	Benign	0.43
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs12248786; hg19: chr10-88512342;