rs2056694

chr7-129283976-C-T

Variant summary

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

The NM_015328.4(AHCYL2):c.363+58537C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,044 control chromosomes in the GnomAD database, including 4,714 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 0.25 (4714 hom., cov: 32)
• Consequence: AHCYL2 NM_015328.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206

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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AHCYL2	NM_015328.4	c.363+58537C>T		intron_variant		ENST00000325006.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AHCYL2	ENST00000325006.8	c.363+58537C>T		intron_variant		1	NM_015328.4
AHCYL2	ENST00000446544.6	c.363+58537C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37577 AN: 151926 Hom.: 4707 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.247 AC: 37598 AN: 152044 Hom.: 4714 Cov.: 32 AF XY: 0.247 AC XY: 18333 AN XY: 74330

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.259

Alfa AF: 0.237 Hom.: 692

Bravo AF: 0.253

Asia WGS AF: 0.337 AC: 1168 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.6
Dann	Benign	0.33

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: rs2056694; hg19: chr7-128923817;