chr11-81273177-G-T

Variant names:

• chr11-81273177-G-T
• rs10897779
• ENST00000671134.1:n.324-1699G>T

Variant summary

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

The ENST00000671134.1(ENSG00000287912):​n.324-1699G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 151,880 control chromosomes in the GnomAD database, including 6,427 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 0.27 (6427 hom., cov: 32)
• Consequence: ENSG00000287912 ENST00000671134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 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.324-1699G>T		intron	N/A
	ENSG00000287912	ENST00000671210.1		n.310-1699G>T		intron	N/A
	ENSG00000287912	ENST00000701193.2		n.196-1699G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41286 AN: 151762 Hom.: 6416 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.272 AC: 41324 AN: 151880 Hom.: 6427 Cov.: 32 AF XY: 0.274 AC XY: 20336 AN XY: 74254

African (AFR) AF: 0.332 AC: 13733 AN: 41356

American (AMR) AF: 0.238 AC: 3629 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 930 AN: 3468

East Asian (EAS) AF: 0.695 AC: 3579 AN: 5150

South Asian (SAS) AF: 0.343 AC: 1652 AN: 4816

European-Finnish (FIN) AF: 0.180 AC: 1902 AN: 10570

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14904 AN: 67962

Other (OTH) AF: 0.283 AC: 597 AN: 2108

Alfa AF: 0.228 Hom.: 6031

Bravo AF: 0.281

Asia WGS AF: 0.491 AC: 1709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.11
DANN	Benign	0.60
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs10897779; hg19: chr11-80984220;