7-129251818-C-T

Variant names:

• chr7-129251818-C-T
• rs721691
• NM_015328.4:c.363+26379C>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+26379C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,064 control chromosomes in the GnomAD database, including 6,606 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 (6606 hom., cov: 31)
• Consequence: AHCYL2 NM_015328.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AHCYL2	NM_015328.4	c.363+26379C>T		intron_variant	Intron 1 of 16	ENST00000325006.8	NP_056143.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AHCYL2	ENST00000325006.8	c.363+26379C>T		intron_variant	Intron 1 of 16	1	NM_015328.4	ENSP00000315931.3
AHCYL2	ENST00000446544.6	c.363+26379C>T		intron_variant	Intron 1 of 16	1		ENSP00000413639.2

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40184 AN: 151946 Hom.: 6607 Cov.: 31

Gnomad AFR AF: 0.0664

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.264 AC: 40185 AN: 152064 Hom.: 6606 Cov.: 31 AF XY: 0.274 AC XY: 20385 AN XY: 74324

Gnomad4 AFR AF: 0.0663

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.271

Alfa AF: 0.278 Hom.: 845

Bravo AF: 0.253

Asia WGS AF: 0.447 AC: 1555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.49

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: rs721691; hg19: chr7-128891659;