chr1-245133143-C-T

Variant names:

• chr1-245133143-C-T
• rs12407427
• ENST00000809837.1:n.244+20411G>A

Variant summary

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

The ENST00000809837.1(ENSG00000305254):​n.244+20411G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,000 control chromosomes in the GnomAD database, including 4,784 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 0.22 (4784 hom., cov: 32)
• Consequence: ENSG00000305254 ENST00000809837.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 3 publications found

Genes affected

ENSG00000305254 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 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
ENSG00000305254	ENST00000809837.1	n.244+20411G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32956 AN: 151882 Hom.: 4751 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.0730

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.217 AC: 33047 AN: 152000 Hom.: 4784 Cov.: 32 AF XY: 0.218 AC XY: 16192 AN XY: 74324

African (AFR) AF: 0.377 AC: 15630 AN: 41410

American (AMR) AF: 0.362 AC: 5514 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 403 AN: 3470

East Asian (EAS) AF: 0.124 AC: 641 AN: 5172

South Asian (SAS) AF: 0.202 AC: 970 AN: 4812

European-Finnish (FIN) AF: 0.0730 AC: 773 AN: 10592

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8554 AN: 67976

Other (OTH) AF: 0.222 AC: 469 AN: 2110

Alfa AF: 0.164 Hom.: 2213

Bravo AF: 0.249

Asia WGS AF: 0.208 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.31
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs12407427; hg19: chr1-245296445;