11-81275763-T-C

Variant names:

• chr11-81275763-T-C
• rs10501500
• ENST00000671134.1:n.428+783T>C

Variant summary

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

The ENST00000671134.1(ENSG00000287912):​n.428+783T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,082 control chromosomes in the GnomAD database, including 2,238 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 0.16 (2238 hom., cov: 32)
• Consequence: ENSG00000287912 ENST00000671134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• Publications: 1 publications found

Genes affected

ENSG00000287912 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671134.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287912	ENST00000671134.1		n.428+783T>C		intron	N/A
	ENSG00000287912	ENST00000701193.2		n.300+783T>C		intron	N/A
	ENSG00000287912	ENST00000825736.1		n.440+783T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24678 AN: 151966 Hom.: 2238 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0975

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.162 AC: 24686 AN: 152082 Hom.: 2238 Cov.: 32 AF XY: 0.159 AC XY: 11831 AN XY: 74354

African (AFR) AF: 0.220 AC: 9119 AN: 41414

American (AMR) AF: 0.125 AC: 1905 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 667 AN: 3468

East Asian (EAS) AF: 0.159 AC: 820 AN: 5172

South Asian (SAS) AF: 0.116 AC: 558 AN: 4820

European-Finnish (FIN) AF: 0.0975 AC: 1034 AN: 10606

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9999 AN: 67994

Other (OTH) AF: 0.175 AC: 371 AN: 2116

Alfa AF: 0.155 Hom.: 3658

Bravo AF: 0.171

Asia WGS AF: 0.104 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.48
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs10501500; hg19: chr11-80986806;