rs11816922

Variant names:

• chr10-6882482-C-A
• rs11816922
• ENST00000652889.2:n.420-18348G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-6882482-C-A
• chr10-6882482-C-T

Variant summary

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

The ENST00000652889.2(ENSG00000287277):​n.420-18348G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 143,180 control chromosomes in the GnomAD database, including 967 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 0.11 (967 hom., cov: 29)
• Consequence: ENSG00000287277 ENST00000652889.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537
• Publications: 4 publications found

Genes affected

ENSG00000287277 (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 (AFR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376387	NR_188183.1	n.568+52631G>T		intron_variant	Intron 3 of 4
LOC105376387	NR_188184.1	n.370+52631G>T		intron_variant	Intron 2 of 4
LOC105376387	NR_188185.1	n.371-31633G>T		intron_variant	Intron 2 of 4
LOC105376387	NR_188186.1	n.370+52631G>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287277	ENST00000652889.2	n.420-18348G>T		intron_variant	Intron 2 of 3
ENSG00000287277	ENST00000654694.1	n.377-18348G>T		intron_variant	Intron 2 of 3
ENSG00000287277	ENST00000664549.1	n.568+52631G>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.108 AC: 15481 AN: 143078 Hom.: 967 Cov.: 29

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.0460

Gnomad AMR AF: 0.0892

Gnomad ASJ AF: 0.0563

Gnomad EAS AF: 0.00117

Gnomad SAS AF: 0.0777

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.0742

Gnomad NFE AF: 0.0848

Gnomad OTH AF: 0.0850

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

GnomAD4 genome AF: 0.108 AC: 15491 AN: 143180 Hom.: 967 Cov.: 29 AF XY: 0.109 AC XY: 7599 AN XY: 69752

African (AFR) AF: 0.168 AC: 6606 AN: 39276

American (AMR) AF: 0.0890 AC: 1291 AN: 14506

Ashkenazi Jewish (ASJ) AF: 0.0563 AC: 192 AN: 3408

East Asian (EAS) AF: 0.00117 AC: 5 AN: 4266

South Asian (SAS) AF: 0.0775 AC: 337 AN: 4346

European-Finnish (FIN) AF: 0.140 AC: 1366 AN: 9760

Middle Eastern (MID) AF: 0.0694 AC: 20 AN: 288

European-Non Finnish (NFE) AF: 0.0848 AC: 5471 AN: 64520

Other (OTH) AF: 0.0840 AC: 163 AN: 1940

Alfa AF: 0.0337 Hom.: 28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.16
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs11816922; hg19: chr10-6924444;