10-46223285-A-T

Variant names:

• chr10-46223285-A-T
• rs1551687

Variant summary

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

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: AHCYP1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.07
• Publications: 3 publications found

Genes affected

AHCYP1 (HGNC:44993): (adenosylhomocysteinase pseudogene 1)

ENSG00000299562 (HGNC:):

ANTXRLP1 (HGNC:45004): (ANTXR like pseudogene 1)

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=-0.69).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AHCYP1		n.46223285A>T		intragenic_variant
ANTXRLP1	NR_103827.1	n.484-3579T>A		intron_variant	Intron 4 of 4
ANTXRLP1	NR_103828.1	n.304-3579T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299562	ENST00000764651.1	n.126+15328T>A		intron_variant	Intron 1 of 2
ENSG00000299578	ENST00000764724.1	n.405-3541T>A		intron_variant	Intron 3 of 3
ENSG00000299578	ENST00000764725.1	n.718-3579T>A		intron_variant	Intron 5 of 5

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	-0.69
CADD	Benign	2.0
DANN	Benign	0.22
PhyloP100		3.1

Splicing

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

Other links and lift over

dbSNP: rs1551687; hg19: chr10-47594521;