rs10501664

Variant names:

• chr11-88368476-A-C
• rs10501664
• ENST00000684900.2:n.213-4761A>C

Your query was ambiguous. Multiple possible variants found:

• chr11-88368476-A-C
• chr11-88368476-A-G
• chr11-88368476-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000684900.2(ENSG00000288018):​n.213-4761A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: ENSG00000288018 ENST00000684900.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 7 publications found

Genes affected

ENSG00000288018 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929174	NR_188508.1	n.174-4761A>C		intron_variant	Intron 1 of 5
LOC101929174	NR_188509.1	n.174-4761A>C		intron_variant	Intron 1 of 3
LOC101929174	NR_188510.1	n.174-4761A>C		intron_variant	Intron 1 of 4
LOC101929174	NR_188511.1	n.174-4761A>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288018	ENST00000684900.2	n.213-4761A>C		intron_variant	Intron 1 of 4
ENSG00000288018	ENST00000689290.2	n.240-4761A>C		intron_variant	Intron 1 of 3
ENSG00000288018	ENST00000690686.2	n.228-4761A>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.51
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs10501664; hg19: chr11-88101644;