rs4731568

Variant names:

• chr7-129264960-C-G
• rs4731568
• NM_015328.4:c.363+39521C>G

Your query was ambiguous. Multiple possible variants found:

• chr7-129264960-C-G
• chr7-129264960-C-T

Variant summary

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

The NM_015328.4(AHCYL2):​c.363+39521C>G 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: AHCYL2 NM_015328.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 2 publications found

Genes affected

AHCYL2 (HGNC:22204): (adenosylhomocysteinase like 2) The protein encoded by this gene acts as a homotetramer and may be involved in the conversion of S-adenosyl-L-homocysteine to L-homocysteine and adenosine. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2011]

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=-0.97).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015328.4. 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
	AHCYL2	NM_015328.4	MANE Select	c.363+39521C>G		intron	N/A	NP_056143.1	Q96HN2-1
	AHCYL2	NM_001130720.3		c.363+39521C>G		intron	N/A	NP_001124192.1	Q96HN2-2
	AHCYL2	NM_001393387.1		c.363+39521C>G		intron	N/A	NP_001380316.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHCYL2	ENST00000325006.8	TSL:1 MANE Select	c.363+39521C>G		intron	N/A	ENSP00000315931.3	Q96HN2-1
	AHCYL2	ENST00000446544.6	TSL:1	c.363+39521C>G		intron	N/A	ENSP00000413639.2	Q96HN2-2
	AHCYL2	ENST00000940561.1		c.363+39521C>G		intron	N/A	ENSP00000610620.1

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.085
DANN	Benign	0.34
PhyloP100		-1.1

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: rs4731568; hg19: chr7-128904801;