2-64332487-G-A

Variant names:

• chr2-64332487-G-A
• rs1365475
• ENST00000448204.3:n.247-268C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000448204.3(ENSG00000238012):​n.247-268C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 151,886 control chromosomes in the GnomAD database, including 24,766 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 0.56 (24766 hom., cov: 31)
• Consequence: ENSG00000238012 ENST00000448204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.973
• Publications: 3 publications found

Genes affected

ENSG00000238012 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374769	NR_187908.1	n.147+146C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000238012	ENST00000448204.3	n.247-268C>T		intron_variant	Intron 1 of 2	3
ENSG00000238012	ENST00000662477.2	n.166+146C>T		intron_variant	Intron 1 of 2
ENSG00000288932	ENST00000717283.1	n.335+8665G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85553 AN: 151768 Hom.: 24745 Cov.: 31

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.564 AC: 85616 AN: 151886 Hom.: 24766 Cov.: 31 AF XY: 0.563 AC XY: 41789 AN XY: 74214

African (AFR) AF: 0.623 AC: 25794 AN: 41376

American (AMR) AF: 0.484 AC: 7391 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1797 AN: 3470

East Asian (EAS) AF: 0.191 AC: 986 AN: 5158

South Asian (SAS) AF: 0.535 AC: 2573 AN: 4810

European-Finnish (FIN) AF: 0.607 AC: 6406 AN: 10552

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38858 AN: 67944

Other (OTH) AF: 0.503 AC: 1059 AN: 2106

Alfa AF: 0.560 Hom.: 94378

Bravo AF: 0.556

Asia WGS AF: 0.369 AC: 1287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.37
DANN	Benign	0.39
PhyloP100		-0.97

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1365475; hg19: chr2-64559621;