1-76018329-G-T

Variant names:

• chr1-76018329-G-T
• rs12753569
• ENST00000436121.3:n.468-805G>T

Variant summary

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

The ENST00000436121.3(ENSG00000225605):​n.468-805G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,936 control chromosomes in the GnomAD database, including 15,241 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 0.41 (15241 hom., cov: 31)
• Consequence: ENSG00000225605 ENST00000436121.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 10 publications found

Genes affected

ENSG00000225605 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927342	NR_125939.1	n.147-805G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225605	ENST00000436121.3	n.468-805G>T		intron_variant	Intron 4 of 4	5
ENSG00000225605	ENST00000635455.1	n.747-805G>T		intron_variant	Intron 7 of 7	5
ENSG00000225605	ENST00000653726.1	n.623-805G>T		intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62405 AN: 151818 Hom.: 15242 Cov.: 31

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.411 AC: 62421 AN: 151936 Hom.: 15241 Cov.: 31 AF XY: 0.420 AC XY: 31171 AN XY: 74250

African (AFR) AF: 0.144 AC: 5954 AN: 41468

American (AMR) AF: 0.460 AC: 7022 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1321 AN: 3472

East Asian (EAS) AF: 0.821 AC: 4223 AN: 5146

South Asian (SAS) AF: 0.639 AC: 3069 AN: 4806

European-Finnish (FIN) AF: 0.569 AC: 6005 AN: 10550

Middle Eastern (MID) AF: 0.338 AC: 98 AN: 290

European-Non Finnish (NFE) AF: 0.492 AC: 33440 AN: 67926

Other (OTH) AF: 0.416 AC: 876 AN: 2104

Alfa AF: 0.447 Hom.: 20763

Bravo AF: 0.389

Asia WGS AF: 0.659 AC: 2290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.72
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs12753569; hg19: chr1-76484014;