10-121121873-A-T

Variant names:

• chr10-121121873-A-T
• rs12771493
• ENST00000741064.1:n.94-2524T>A

Variant summary

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

The ENST00000741064.1(ENSG00000296663):​n.94-2524T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,270 control chromosomes in the GnomAD database, including 1,529 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 0.13 (1529 hom., cov: 33)
• Consequence: ENSG00000296663 ENST00000741064.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.809
• Publications: 1 publications found

Genes affected

ENSG00000296663 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902515	XR_007062317.1	n.168-2524T>A		intron_variant	Intron 1 of 1
LOC124902515	XR_007062318.1	n.159-2524T>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296663	ENST00000741064.1	n.94-2524T>A		intron_variant	Intron 1 of 1
ENSG00000296663	ENST00000741065.1	n.85-2524T>A		intron_variant	Intron 1 of 1
ENSG00000296663	ENST00000741066.1	n.238-2524T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19299 AN: 152152 Hom.: 1528 Cov.: 33

Gnomad AFR AF: 0.0332

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.0962

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.127 AC: 19306 AN: 152270 Hom.: 1529 Cov.: 33 AF XY: 0.127 AC XY: 9439 AN XY: 74440

African (AFR) AF: 0.0331 AC: 1377 AN: 41578

American (AMR) AF: 0.152 AC: 2324 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 653 AN: 3470

East Asian (EAS) AF: 0.170 AC: 881 AN: 5178

South Asian (SAS) AF: 0.0971 AC: 468 AN: 4820

European-Finnish (FIN) AF: 0.176 AC: 1868 AN: 10586

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11182 AN: 68010

Other (OTH) AF: 0.153 AC: 323 AN: 2114

Alfa AF: 0.132 Hom.: 208

Bravo AF: 0.123

Asia WGS AF: 0.158 AC: 548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	15
DANN	Benign	0.79
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs12771493; hg19: chr10-122881387;