rs10765573

Variant names:

• chr11-92950166-T-A
• rs10765573
• ENST00000532770.2:n.147-10059T>A

Variant summary

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

The ENST00000532770.2(ENSG00000254874):​n.147-10059T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,112 control chromosomes in the GnomAD database, including 10,541 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 0.37 (10541 hom., cov: 32)
• Consequence: ENSG00000254874 ENST00000532770.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 11 publications found

Genes affected

ENSG00000254874 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 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
ENSG00000254874	ENST00000532770.2	n.147-10059T>A		intron_variant	Intron 1 of 3	2
ENSG00000254874	ENST00000749785.1	n.129-10059T>A		intron_variant	Intron 1 of 2
ENSG00000254874	ENST00000749786.1	n.116-10059T>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56116 AN: 151994 Hom.: 10537 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.369 AC: 56161 AN: 152112 Hom.: 10541 Cov.: 32 AF XY: 0.370 AC XY: 27506 AN XY: 74340

African (AFR) AF: 0.423 AC: 17540 AN: 41492

American (AMR) AF: 0.287 AC: 4386 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1102 AN: 3470

East Asian (EAS) AF: 0.446 AC: 2302 AN: 5164

South Asian (SAS) AF: 0.399 AC: 1923 AN: 4818

European-Finnish (FIN) AF: 0.398 AC: 4201 AN: 10566

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.344 AC: 23376 AN: 67986

Other (OTH) AF: 0.372 AC: 787 AN: 2114

Alfa AF: 0.359 Hom.: 1222

Bravo AF: 0.361

Asia WGS AF: 0.364 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.76
PhyloP100		-0.099

Splicing

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

Other links and lift over

dbSNP: rs10765573; hg19: chr11-92683332;