10-37026293-T-C

Variant names:

• chr10-37026293-T-C
• rs11010995
• ENST00000836532.1:n.268-10384A>G

Variant summary

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

The ENST00000836532.1(ENSG00000308811):​n.268-10384A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0606 in 152,148 control chromosomes in the GnomAD database, including 344 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 0.061 (344 hom., cov: 32)
• Consequence: ENSG00000308811 ENST00000836532.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273
• Publications: 2 publications found

Genes affected

ENSG00000308811 (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 (EAS) allele frequency at 95% confidence interval = 0.0916 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
ENSG00000308811	ENST00000836532.1	n.268-10384A>G		intron_variant	Intron 2 of 2
ENSG00000308811	ENST00000836533.1	n.148-10384A>G		intron_variant	Intron 1 of 1
ENSG00000308811	ENST00000836534.1	n.446+9628A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0607 AC: 9229 AN: 152030 Hom.: 344 Cov.: 32

Gnomad AFR AF: 0.0226

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0746

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0986

Gnomad SAS AF: 0.0573

Gnomad FIN AF: 0.0430

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0757

Gnomad OTH AF: 0.0841

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

GnomAD4 genome AF: 0.0606 AC: 9226 AN: 152148 Hom.: 344 Cov.: 32 AF XY: 0.0591 AC XY: 4397 AN XY: 74398

African (AFR) AF: 0.0225 AC: 935 AN: 41550

American (AMR) AF: 0.0745 AC: 1136 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 479 AN: 3468

East Asian (EAS) AF: 0.0987 AC: 510 AN: 5168

South Asian (SAS) AF: 0.0572 AC: 275 AN: 4810

European-Finnish (FIN) AF: 0.0430 AC: 457 AN: 10616

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.0757 AC: 5145 AN: 67968

Other (OTH) AF: 0.0842 AC: 178 AN: 2114

Alfa AF: 0.0772 Hom.: 717

Bravo AF: 0.0640

Asia WGS AF: 0.100 AC: 349 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	2.4
DANN	Benign	0.59
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs11010995; hg19: chr10-37315221;