rs10504861

Variant names:

• chr8-88535703-C-A
• rs10504861
• ENST00000521433.1:n.180-6977C>A

Your query was ambiguous. Multiple possible variants found:

• chr8-88535703-C-A
• chr8-88535703-C-G
• chr8-88535703-C-T

Variant summary

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

The ENST00000521433.1(ENSG00000253553):​n.180-6977C>A 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: 32)
• Consequence: ENSG00000253553 ENST00000521433.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 0 publications found

Genes affected

ENSG00000253553 (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=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375629	XR_001745651.3	n.676+10814G>T		intron_variant	Intron 6 of 6
LOC105375630	XR_001745653.3	n.225-6977C>A		intron_variant	Intron 2 of 7
LOC105375630	XR_007060996.1	n.180-6977C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253553	ENST00000521433.1	n.180-6977C>A		intron_variant	Intron 2 of 4	4
ENSG00000253553	ENST00000658256.1	n.285-164589C>A		intron_variant	Intron 2 of 3
ENSG00000253553	ENST00000658283.1	n.426-6977C>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.069
DANN	Benign	0.40
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10504861; hg19: chr8-89547932;