1-173063477-G-C

Variant names:

• chr1-173063477-G-C
• rs957544
• ENST00000432694.2:n.666-396G>C

Variant summary

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

The ENST00000432694.2(ENSG00000224000):​n.666-396G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 151,864 control chromosomes in the GnomAD database, including 5,151 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 0.22 (5151 hom., cov: 31)
• Consequence: ENSG00000224000 ENST00000432694.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 2 publications found

Genes affected

ENSG00000224000 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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
ENSG00000224000	ENST00000432694.2	n.666-396G>C		intron_variant	Intron 4 of 4	3
ENSG00000224000	ENST00000717048.1	n.324-396G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32884 AN: 151746 Hom.: 5159 Cov.: 31

Gnomad AFR AF: 0.0710

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.217 AC: 32881 AN: 151864 Hom.: 5151 Cov.: 31 AF XY: 0.223 AC XY: 16569 AN XY: 74226

African (AFR) AF: 0.0709 AC: 2940 AN: 41482

American (AMR) AF: 0.308 AC: 4690 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1077 AN: 3466

East Asian (EAS) AF: 0.753 AC: 3860 AN: 5126

South Asian (SAS) AF: 0.472 AC: 2272 AN: 4810

European-Finnish (FIN) AF: 0.195 AC: 2057 AN: 10540

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.222 AC: 15093 AN: 67904

Other (OTH) AF: 0.253 AC: 534 AN: 2108

Alfa AF: 0.0959 Hom.: 147

Bravo AF: 0.221

Asia WGS AF: 0.535 AC: 1858 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.22
DANN	Benign	0.60
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs957544; hg19: chr1-173032617;