chr1-110000463-T-C

Variant names:

• chr1-110000463-T-C
• rs7553933
• NM_006621.7:c.121-8571T>C

Variant summary

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

The NM_006621.7(AHCYL1):​c.121-8571T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,224 control chromosomes in the GnomAD database, including 2,989 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 0.11 (2989 hom., cov: 32)
• Consequence: AHCYL1 NM_006621.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 2 publications found

Genes affected

AHCYL1 (HGNC:344): (adenosylhomocysteinase like 1) The protein encoded by this gene interacts with inositol 1,4,5-trisphosphate receptor, type 1 and may be involved in the conversion of S-adenosyl-L-homocysteine to L-homocysteine and adenosine. Several transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jun 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006621.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHCYL1	NM_006621.7	MANE Select	c.121-8571T>C		intron	N/A	NP_006612.2
	AHCYL1	NM_001242673.2		c.-21-8571T>C		intron	N/A	NP_001229602.1	O43865-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHCYL1	ENST00000369799.10	TSL:1 MANE Select	c.121-8571T>C		intron	N/A	ENSP00000358814.5	O43865-1
	AHCYL1	ENST00000972197.1		c.121-8571T>C		intron	N/A	ENSP00000642256.1
	AHCYL1	ENST00000972196.1		c.121-8571T>C		intron	N/A	ENSP00000642255.1

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17263 AN: 152106 Hom.: 2971 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0437

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0455

Gnomad FIN AF: 0.00330

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0105

Gnomad OTH AF: 0.0779

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

GnomAD4 genome AF: 0.114 AC: 17317 AN: 152224 Hom.: 2989 Cov.: 32 AF XY: 0.110 AC XY: 8169 AN XY: 74458

African (AFR) AF: 0.372 AC: 15428 AN: 41478

American (AMR) AF: 0.0435 AC: 666 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3462

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5194

South Asian (SAS) AF: 0.0456 AC: 220 AN: 4828

European-Finnish (FIN) AF: 0.00330 AC: 35 AN: 10622

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0105 AC: 711 AN: 68012

Other (OTH) AF: 0.0771 AC: 163 AN: 2114

Alfa AF: 0.0431 Hom.: 410

Bravo AF: 0.128

Asia WGS AF: 0.0570 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	7.2
DANN	Benign	0.58
PhyloP100		0.078
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7553933; hg19: chr1-110543085;