rs3828329

Variant names:

• chr2-279705-C-A
• rs3828329
• NM_001002919.3:c.*442G>T

Your query was ambiguous. Multiple possible variants found:

• chr2-279705-C-A
• chr2-279705-C-G
• chr2-279705-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001002919.3(ALKAL2):​c.*442G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ALKAL2 NM_001002919.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.575
• Publications: 20 publications found

Genes affected

ALKAL2 (HGNC:27683): (ALK and LTK ligand 2) Enables receptor signaling protein tyrosine kinase activator activity and receptor tyrosine kinase binding activity. Involved in positive regulation of ERK1 and ERK2 cascade; positive regulation of ERK5 cascade; and positive regulation of neuron projection development. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALKAL2	NM_001002919.3	c.*442G>T		3_prime_UTR_variant	Exon 6 of 6	ENST00000403610.9	NP_001002919.2
ALKAL2	XM_047443980.1	c.*442G>T		3_prime_UTR_variant	Exon 6 of 6		XP_047299936.1
ALKAL2	XM_047443981.1	c.*442G>T		3_prime_UTR_variant	Exon 5 of 5		XP_047299937.1
ALKAL2	XM_047443982.1	c.*442G>T		3_prime_UTR_variant	Exon 5 of 5		XP_047299938.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALKAL2	ENST00000403610.9	c.*442G>T		3_prime_UTR_variant	Exon 6 of 6	1	NM_001002919.3	ENSP00000384604.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 11800 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6178

African (AFR) AF: 0.00 AC: 0 AN: 410

American (AMR) AF: 0.00 AC: 0 AN: 1440

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 390

East Asian (EAS) AF: 0.00 AC: 0 AN: 850

South Asian (SAS) AF: 0.00 AC: 0 AN: 802

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 666

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 22

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 6708

Other (OTH) AF: 0.00 AC: 0 AN: 512

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.4
DANN	Benign	0.49
PhyloP100		0.57

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

Other links and lift over

dbSNP: rs3828329; hg19: chr2-279705;