10-6882482-C-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000652889.2(ENSG00000287277):​n.420-18348G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000698 in 143,190 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000070 (0 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376387	NR_188183.1	n.568+52631G>A		intron_variant	Intron 3 of 4
LOC105376387	NR_188184.1	n.370+52631G>A		intron_variant	Intron 2 of 4
LOC105376387	NR_188185.1	n.371-31633G>A		intron_variant	Intron 2 of 4
LOC105376387	NR_188186.1	n.370+52631G>A		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>A		intron_variant	Intron 2 of 3
ENSG00000287277	ENST00000654694.1	n.377-18348G>A		intron_variant	Intron 2 of 3
ENSG00000287277	ENST00000664549.1	n.568+52631G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.0000698 AC: 10 AN: 143190 Hom.: 0 Cov.: 29

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000690

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000234

Gnomad SAS AF: 0.00184

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000698 AC: 10 AN: 143190 Hom.: 0 Cov.: 29 AF XY: 0.000115 AC XY: 8 AN XY: 69696

African (AFR) AF: 0.00 AC: 0 AN: 39200

American (AMR) AF: 0.0000690 AC: 1 AN: 14498

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3410

East Asian (EAS) AF: 0.000234 AC: 1 AN: 4274

South Asian (SAS) AF: 0.00184 AC: 8 AN: 4356

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9774

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 310

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 64566

Other (OTH) AF: 0.00 AC: 0 AN: 1932

Alfa AF: 0.00 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	1.8
DANN	Benign	0.14
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;