rs7787531

Positions:

• chr7-129383756-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.475+4007C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.879 in 152,108 control chromosomes in the GnomAD database, including 59,234 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 0.88 (59234 hom., cov: 29)
• Consequence: AHCYL2 NM_015328.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160

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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AHCYL2	NM_015328.4	c.475+4007C>T		intron_variant		ENST00000325006.8	NP_056143.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AHCYL2	ENST00000325006.8	c.475+4007C>T		intron_variant		1	NM_015328.4	ENSP00000315931

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133654 AN: 151990 Hom.: 59193 Cov.: 29

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.959

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.889

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

GnomAD4 genome AF: 0.879 AC: 133749 AN: 152108 Hom.: 59234 Cov.: 29 AF XY: 0.882 AC XY: 65590 AN XY: 74356

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.934

Gnomad4 ASJ AF: 0.897

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.890

Gnomad4 FIN AF: 0.959

Gnomad4 NFE AF: 0.921

Gnomad4 OTH AF: 0.890

Alfa AF: 0.918 Hom.: 115244

Bravo AF: 0.872

Asia WGS AF: 0.936 AC: 3256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.81
DANN	Benign	0.88

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: rs7787531; hg19: chr7-129023597;