1-168393090-G-C

Variant names:

• chr1-168393090-G-C
• rs16860501
• ENST00000823032.1:n.312+13308G>C

Variant summary

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

The ENST00000823032.1(ENSG00000307038):​n.312+13308G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0792 in 152,250 control chromosomes in the GnomAD database, including 604 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 0.079 (604 hom., cov: 32)
• Consequence: ENSG00000307038 ENST00000823032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292
• Publications: 1 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.113 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.312+13308G>C		intron_variant	Intron 2 of 2
ENSG00000307038	ENST00000823033.1	n.303+13308G>C		intron_variant	Intron 2 of 3
ENSG00000307038	ENST00000823034.1	n.536+13308G>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0793 AC: 12057 AN: 152132 Hom.: 602 Cov.: 32

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0682

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0345

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0880

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

GnomAD4 genome AF: 0.0792 AC: 12060 AN: 152250 Hom.: 604 Cov.: 32 AF XY: 0.0808 AC XY: 6017 AN XY: 74422

African (AFR) AF: 0.0275 AC: 1143 AN: 41564

American (AMR) AF: 0.0681 AC: 1042 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3472

East Asian (EAS) AF: 0.0347 AC: 180 AN: 5182

South Asian (SAS) AF: 0.121 AC: 583 AN: 4810

European-Finnish (FIN) AF: 0.149 AC: 1573 AN: 10592

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6948 AN: 68012

Other (OTH) AF: 0.0885 AC: 187 AN: 2112

Alfa AF: 0.0378 Hom.: 36

Bravo AF: 0.0684

Asia WGS AF: 0.0840 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.83
DANN	Benign	0.41
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs16860501; hg19: chr1-168362328;