1-38594823-G-A

Variant names:

• chr1-38594823-G-A
• rs12026014
• ENST00000733464.1:n.461+19107C>T

Variant summary

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

The ENST00000733464.1(ENSG00000295881):​n.461+19107C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 149,882 control chromosomes in the GnomAD database, including 11,555 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 0.39 (11555 hom., cov: 26)
• Consequence: ENSG00000295881 ENST00000733464.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 3 publications found

Genes affected

ENSG00000295881 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000733464.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295881	ENST00000733464.1		n.461+19107C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.385 AC: 57716 AN: 149764 Hom.: 11542 Cov.: 26

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.385 AC: 57752 AN: 149882 Hom.: 11555 Cov.: 26 AF XY: 0.390 AC XY: 28484 AN XY: 73004

African (AFR) AF: 0.287 AC: 11677 AN: 40622

American (AMR) AF: 0.492 AC: 7362 AN: 14966

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1760 AN: 3458

East Asian (EAS) AF: 0.583 AC: 2955 AN: 5066

South Asian (SAS) AF: 0.420 AC: 1953 AN: 4646

European-Finnish (FIN) AF: 0.415 AC: 4274 AN: 10290

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26572 AN: 67582

Other (OTH) AF: 0.416 AC: 856 AN: 2060

Alfa AF: 0.393 Hom.: 21469

Bravo AF: 0.388

Asia WGS AF: 0.441 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.41
PhyloP100		-0.075

Splicing

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

Other links and lift over

dbSNP: rs12026014; hg19: chr1-39060495;