rs1551687

Variant names:

• chr10-46223285-A-C
• rs1551687

Your query was ambiguous. Multiple possible variants found:

• chr10-46223285-A-C
• chr10-46223285-A-G
• chr10-46223285-A-T

Variant summary

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

The variant allele was found at a frequency of 0.423 in 151,520 control chromosomes in the GnomAD database, including 13,698 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 0.42 (13698 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AHCYP1		n.46223285A>C		intragenic_variant
ANTXRLP1	NR_103827.1	n.484-3579T>G		intron_variant	Intron 4 of 4
ANTXRLP1	NR_103828.1	n.304-3579T>G		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>G		intron_variant	Intron 1 of 2
ENSG00000299578	ENST00000764724.1	n.405-3541T>G		intron_variant	Intron 3 of 3
ENSG00000299578	ENST00000764725.1	n.718-3579T>G		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64002 AN: 151400 Hom.: 13671 Cov.: 33

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.423 AC: 64080 AN: 151520 Hom.: 13698 Cov.: 33 AF XY: 0.425 AC XY: 31472 AN XY: 74080

African (AFR) AF: 0.528 AC: 21683 AN: 41074

American (AMR) AF: 0.491 AC: 7488 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1536 AN: 3464

East Asian (EAS) AF: 0.574 AC: 2945 AN: 5128

South Asian (SAS) AF: 0.289 AC: 1391 AN: 4818

European-Finnish (FIN) AF: 0.389 AC: 4112 AN: 10582

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.348 AC: 23593 AN: 67892

Other (OTH) AF: 0.421 AC: 889 AN: 2112

Alfa AF: 0.392 Hom.: 1519

Bravo AF: 0.441

Asia WGS AF: 0.470 AC: 1634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	2.3
DANN	Benign	0.35
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;