rs632407

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904565	XR_007066966.1	n.65-3179C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234464	ENST00000716151.1	n.548-3179C>T		intron_variant	Intron 5 of 7
ENSG00000234464	ENST00000716155.1	n.506+446C>T		intron_variant	Intron 6 of 8

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 v4.3

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;