7-129264960-C-T

Position:

• chr7-129264960-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+39521C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,106 control chromosomes in the GnomAD database, including 6,285 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 0.26 (6285 hom., cov: 33)
• Consequence: AHCYL2 NM_015328.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AHCYL2	NM_015328.4	c.363+39521C>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.363+39521C>T		intron_variant		1	NM_015328.4	ENSP00000315931.3
AHCYL2	ENST00000446544.6	c.363+39521C>T		intron_variant		1		ENSP00000413639.2

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39109 AN: 151988 Hom.: 6286 Cov.: 33

Gnomad AFR AF: 0.0634

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.257 AC: 39111 AN: 152106 Hom.: 6285 Cov.: 33 AF XY: 0.266 AC XY: 19792 AN XY: 74350

Gnomad4 AFR AF: 0.0633

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.264

Alfa AF: 0.260 Hom.: 1321

Bravo AF: 0.247

Asia WGS AF: 0.438 AC: 1523 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.39

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: rs4731568; hg19: chr7-128904801;