rs1665105

chr7-129429137-G-Achr7-129429137-G-Cchr7-129429137-G-T

Variant summary

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

The NM_015328.4(AHCYL2):c.*2092G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 152,022 control chromosomes in the GnomAD database, including 16,022 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 0.46 (16022 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: AHCYL2 NM_015328.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AHCYL2	NM_015328.4	c.*2092G>A		3_prime_UTR_variant	17/17	ENST00000325006.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AHCYL2	ENST00000325006.8	c.*2092G>A		3_prime_UTR_variant	17/17	1	NM_015328.4
AHCYL2	ENST00000446544.6	c.*2092G>A		3_prime_UTR_variant	17/17	1

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69318 AN: 151904 Hom.: 16014 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.521

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.456 AC: 69357 AN: 152022 Hom.: 16022 Cov.: 32 AF XY: 0.454 AC XY: 33697 AN XY: 74304

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.518

Alfa AF: 0.455 Hom.: 22540

Bravo AF: 0.464

Asia WGS AF: 0.432 AC: 1504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.0040
Dann	Benign	0.45

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: rs1665105; hg19: chr7-129068978;