10-57215048-C-G

Variant names:

• chr10-57215048-C-G
• rs11005694
• ENST00000690550.2:n.146+7564G>C

Variant summary

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

The ENST00000690550.2(ENSG00000289158):​n.146+7564G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,776 control chromosomes in the GnomAD database, including 22,095 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 0.49 (22095 hom., cov: 32)
• Consequence: ENSG00000289158 ENST00000690550.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440
• Publications: 3 publications found

Genes affected

ENSG00000289158 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 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
ENSG00000289158	ENST00000690550.2	n.146+7564G>C		intron_variant	Intron 1 of 2
ENSG00000289158	ENST00000752897.1	n.151+7564G>C		intron_variant	Intron 1 of 3
ENSG00000289158	ENST00000752899.1	n.66+7564G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74604 AN: 151658 Hom.: 22047 Cov.: 32

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.492 AC: 74715 AN: 151776 Hom.: 22095 Cov.: 32 AF XY: 0.486 AC XY: 36045 AN XY: 74134

African (AFR) AF: 0.840 AC: 34872 AN: 41492

American (AMR) AF: 0.374 AC: 5692 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 926 AN: 3464

East Asian (EAS) AF: 0.179 AC: 927 AN: 5168

South Asian (SAS) AF: 0.397 AC: 1916 AN: 4824

European-Finnish (FIN) AF: 0.347 AC: 3645 AN: 10518

Middle Eastern (MID) AF: 0.497 AC: 144 AN: 290

European-Non Finnish (NFE) AF: 0.372 AC: 25222 AN: 67806

Other (OTH) AF: 0.459 AC: 965 AN: 2102

Alfa AF: 0.409 Hom.: 1849

Bravo AF: 0.511

Asia WGS AF: 0.354 AC: 1227 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.36
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs11005694; hg19: chr10-58974808;