rs4110091

chr7-129292908-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015328.4(AHCYL2):c.363+67469A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,258 control chromosomes in the GnomAD database, including 1,850 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 0.14 (1850 hom., cov: 32)
• Consequence: AHCYL2 NM_015328.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AHCYL2	NM_015328.4	c.363+67469A>G		intron_variant		ENST00000325006.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AHCYL2	ENST00000325006.8	c.363+67469A>G		intron_variant		1	NM_015328.4
AHCYL2	ENST00000446544.6	c.363+67469A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21543 AN: 152140 Hom.: 1850 Cov.: 32

Gnomad AFR AF: 0.0413

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.141 AC: 21532 AN: 152258 Hom.: 1850 Cov.: 32 AF XY: 0.140 AC XY: 10411 AN XY: 74440

Gnomad4 AFR AF: 0.0412

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.140

Alfa AF: 0.186 Hom.: 3622

Bravo AF: 0.133

Asia WGS AF: 0.181 AC: 629 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	3.0
Dann	Benign	0.79

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

Publications

LitVar

Other links and lift over

dbSNP: rs4110091; hg19: chr7-128932749;