1-157939735-C-T

Variant names:

• chr1-157939735-C-T
• rs1925035
• ENST00000422062.1:n.262-2929C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000422062.1(ENSG00000291226):​n.262-2929C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 152,006 control chromosomes in the GnomAD database, including 9,064 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 0.32 (9064 hom., cov: 31)
• Consequence: ENSG00000291226 ENST00000422062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297

Genes affected

ENSG00000291226 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371458	NR_135760.1	n.340-5921C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291226	ENST00000422062.1	n.262-2929C>T		intron_variant	Intron 1 of 1	2
ENSG00000291226	ENST00000452528.5	n.333-5921C>T		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49169 AN: 151888 Hom.: 9051 Cov.: 31

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.324 AC: 49181 AN: 152006 Hom.: 9064 Cov.: 31 AF XY: 0.329 AC XY: 24435 AN XY: 74296

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.576

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.356

Alfa AF: 0.362 Hom.: 20944

Bravo AF: 0.326

Asia WGS AF: 0.451 AC: 1569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1925035; hg19: chr1-157909525;