1-34485995-C-T

Variant names:

• chr1-34485995-C-T
• rs3905173
• ENST00000824030.1:n.137-16009G>A

Variant summary

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

The ENST00000824030.1(ENSG00000307130):​n.137-16009G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,022 control chromosomes in the GnomAD database, including 28,819 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 0.61 (28819 hom., cov: 32)
• Consequence: ENSG00000307130 ENST00000824030.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 3 publications found

Genes affected

ENSG00000307130 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824030.1. 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
	ENSG00000307130	ENST00000824030.1		n.137-16009G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92318 AN: 151904 Hom.: 28791 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.608 AC: 92391 AN: 152022 Hom.: 28819 Cov.: 32 AF XY: 0.617 AC XY: 45855 AN XY: 74276

African (AFR) AF: 0.519 AC: 21513 AN: 41446

American (AMR) AF: 0.703 AC: 10728 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2258 AN: 3470

East Asian (EAS) AF: 0.987 AC: 5105 AN: 5174

South Asian (SAS) AF: 0.666 AC: 3207 AN: 4818

European-Finnish (FIN) AF: 0.708 AC: 7476 AN: 10556

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40150 AN: 67974

Other (OTH) AF: 0.608 AC: 1285 AN: 2112

Alfa AF: 0.586 Hom.: 13373

Bravo AF: 0.602

Asia WGS AF: 0.819 AC: 2845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.8
DANN	Benign	0.70
PhyloP100		0.0090

Splicing

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

Other links and lift over

dbSNP: rs3905173; hg19: chr1-34951596;