chr1-230539080-T-C

Variant names:

• chr1-230539080-T-C
• rs701157
• ENST00000685406.1:n.242-37414T>C

Variant summary

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

The ENST00000685406.1(ENSG00000282564):​n.242-37414T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,874 control chromosomes in the GnomAD database, including 19,649 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 0.50 (19649 hom., cov: 31)
• Consequence: ENSG00000282564 ENST00000685406.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306

Genes affected

ENSG00000282564 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 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
ENSG00000282564	ENST00000685406.1	n.242-37414T>C		intron_variant	Intron 2 of 5
ENSG00000282564	ENST00000689608.1	n.329+40114T>C		intron_variant	Intron 2 of 3
ENSG00000282564	ENST00000692577.2	n.318+40114T>C		intron_variant	Intron 2 of 4
ENSG00000282564	ENST00000702785.1	n.263+40114T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76347 AN: 151758 Hom.: 19614 Cov.: 31

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.503 AC: 76436 AN: 151874 Hom.: 19649 Cov.: 31 AF XY: 0.507 AC XY: 37607 AN XY: 74204

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.484

Alfa AF: 0.454 Hom.: 28162

Bravo AF: 0.519

Asia WGS AF: 0.623 AC: 2168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.3
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs701157; hg19: chr1-230674826;