1-172884320-C-T

Variant names:

• chr1-172884320-C-T
• rs7517810
• ENST00000432694.2:n.223+108193C>T

Variant summary

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

The ENST00000432694.2(ENSG00000224000):​n.223+108193C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,988 control chromosomes in the GnomAD database, including 8,274 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 0.30 (8274 hom., cov: 32)
• Consequence: ENSG00000224000 ENST00000432694.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889
• Publications: 45 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000432694.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000224000	ENST00000432694.2	TSL:3	n.223+108193C>T		intron	N/A
	ENSG00000224000	ENST00000717047.1		n.354-15646C>T		intron	N/A
	ENSG00000224000	ENST00000717048.1		n.323+621C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45922 AN: 151872 Hom.: 8269 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.302 AC: 45939 AN: 151988 Hom.: 8274 Cov.: 32 AF XY: 0.312 AC XY: 23148 AN XY: 74300

African (AFR) AF: 0.275 AC: 11414 AN: 41470

American (AMR) AF: 0.455 AC: 6943 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 914 AN: 3470

East Asian (EAS) AF: 0.866 AC: 4469 AN: 5158

South Asian (SAS) AF: 0.413 AC: 1995 AN: 4826

European-Finnish (FIN) AF: 0.295 AC: 3116 AN: 10564

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.238 AC: 16201 AN: 67946

Other (OTH) AF: 0.310 AC: 653 AN: 2108

Alfa AF: 0.274 Hom.: 28799

Bravo AF: 0.321

Asia WGS AF: 0.544 AC: 1892 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.87
DANN	Benign	0.65
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs7517810; hg19: chr1-172853460;