1-168532215-A-G

Variant names:

• chr1-168532215-A-G
• rs10429892
• ENST00000823032.1:n.313-44047A>G

Variant summary

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

The ENST00000823032.1(ENSG00000307038):​n.313-44047A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 152,142 control chromosomes in the GnomAD database, including 26,324 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 0.58 (26324 hom., cov: 32)
• Consequence: ENSG00000307038 ENST00000823032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 3 publications found

Genes affected

ENSG00000307038 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.845 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
ENSG00000307038	ENST00000823032.1	n.313-44047A>G		intron_variant	Intron 2 of 2
ENSG00000307038	ENST00000823033.1	n.304-11672A>G		intron_variant	Intron 2 of 3
ENSG00000307038	ENST00000823034.1	n.537-11672A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88213 AN: 152024 Hom.: 26287 Cov.: 32

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.580 AC: 88306 AN: 152142 Hom.: 26324 Cov.: 32 AF XY: 0.592 AC XY: 44048 AN XY: 74384

African (AFR) AF: 0.641 AC: 26601 AN: 41494

American (AMR) AF: 0.632 AC: 9670 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1988 AN: 3472

East Asian (EAS) AF: 0.866 AC: 4486 AN: 5182

South Asian (SAS) AF: 0.653 AC: 3149 AN: 4820

European-Finnish (FIN) AF: 0.669 AC: 7091 AN: 10594

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33389 AN: 67966

Other (OTH) AF: 0.603 AC: 1277 AN: 2116

Alfa AF: 0.520 Hom.: 35285

Bravo AF: 0.584

Asia WGS AF: 0.751 AC: 2613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.1
DANN	Benign	0.50
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs10429892; hg19: chr1-168501453;