chr1-238613962-C-T

Variant names:

• chr1-238613962-C-T
• rs632407
• ENST00000716151.1:n.548-3179C>T

Variant summary

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

The ENST00000716151.1(ENSG00000234464):​n.548-3179C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.034 in 152,200 control chromosomes in the GnomAD database, including 135 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 0.034 (135 hom., cov: 33)
• Consequence: ENSG00000234464 ENST00000716151.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.627
• Publications: 1 publications found

Genes affected

ENSG00000234464 (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 (NFE) allele frequency at 95% confidence interval = 0.0503 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716151.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234464	ENST00000716151.1		n.548-3179C>T		intron	N/A
	ENSG00000234464	ENST00000716155.1		n.506+446C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0340 AC: 5175 AN: 152082 Hom.: 135 Cov.: 33

Gnomad AFR AF: 0.00918

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.0279

Gnomad ASJ AF: 0.0182

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00933

Gnomad FIN AF: 0.0607

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0517

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0340 AC: 5174 AN: 152200 Hom.: 135 Cov.: 33 AF XY: 0.0340 AC XY: 2533 AN XY: 74412

African (AFR) AF: 0.00915 AC: 380 AN: 41534

American (AMR) AF: 0.0279 AC: 426 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0182 AC: 63 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00934 AC: 45 AN: 4820

European-Finnish (FIN) AF: 0.0607 AC: 643 AN: 10596

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0517 AC: 3518 AN: 67998

Other (OTH) AF: 0.0284 AC: 60 AN: 2110

Alfa AF: 0.0421 Hom.: 20

Bravo AF: 0.0299

Asia WGS AF: 0.00462 AC: 17 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.6
DANN	Benign	0.65
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs632407; hg19: chr1-238777262;