1-73359226-A-G

Variant names:

• chr1-73359226-A-G
• rs10789369
• ENST00000729649.1:n.85-16707T>C

Variant summary

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

The ENST00000729649.1(ENSG00000295376):​n.85-16707T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 151,980 control chromosomes in the GnomAD database, including 30,048 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 0.62 (30048 hom., cov: 31)
• Consequence: ENSG00000295376 ENST00000729649.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 21 publications found

Genes affected

ENSG00000295376 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295376	ENST00000729649.1	n.85-16707T>C		intron_variant	Intron 1 of 2
ENSG00000295376	ENST00000729650.1	n.85-16707T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94638 AN: 151862 Hom.: 30019 Cov.: 31

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.623 AC: 94711 AN: 151980 Hom.: 30048 Cov.: 31 AF XY: 0.623 AC XY: 46252 AN XY: 74268

African (AFR) AF: 0.695 AC: 28815 AN: 41444

American (AMR) AF: 0.458 AC: 6987 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1928 AN: 3470

East Asian (EAS) AF: 0.773 AC: 3987 AN: 5156

South Asian (SAS) AF: 0.656 AC: 3155 AN: 4806

European-Finnish (FIN) AF: 0.634 AC: 6703 AN: 10572

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.605 AC: 41124 AN: 67962

Other (OTH) AF: 0.586 AC: 1234 AN: 2106

Alfa AF: 0.580 Hom.: 29413

Bravo AF: 0.610

Asia WGS AF: 0.677 AC: 2352 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.59
DANN	Benign	0.11
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10789369; hg19: chr1-73824909;