rs17126268

Variant names:

• chr1-102260843-T-C
• rs17126268
• ENST00000447916.1:n.398+49427A>G

Variant summary

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

The ENST00000447916.1(ENSG00000233359):​n.398+49427A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0716 in 151,930 control chromosomes in the GnomAD database, including 446 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 0.072 (446 hom., cov: 32)
• Consequence: ENSG00000233359 ENST00000447916.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 3 publications found

Genes affected

ENSG00000233359 (HGNC:58374):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0968 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
ENSG00000233359	ENST00000447916.1	n.398+49427A>G		intron_variant	Intron 5 of 5	3
ENSG00000233359	ENST00000656454.1	n.104-35432A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0716 AC: 10872 AN: 151812 Hom.: 445 Cov.: 32

Gnomad AFR AF: 0.0993

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0512

Gnomad ASJ AF: 0.0770

Gnomad EAS AF: 0.00136

Gnomad SAS AF: 0.0686

Gnomad FIN AF: 0.0217

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0733

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0716 AC: 10881 AN: 151930 Hom.: 446 Cov.: 32 AF XY: 0.0674 AC XY: 5000 AN XY: 74228

African (AFR) AF: 0.0994 AC: 4122 AN: 41484

American (AMR) AF: 0.0510 AC: 776 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.0770 AC: 267 AN: 3468

East Asian (EAS) AF: 0.00136 AC: 7 AN: 5138

South Asian (SAS) AF: 0.0678 AC: 327 AN: 4824

European-Finnish (FIN) AF: 0.0217 AC: 230 AN: 10594

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0732 AC: 4973 AN: 67896

Other (OTH) AF: 0.0621 AC: 131 AN: 2110

Alfa AF: 0.0739 Hom.: 654

Bravo AF: 0.0755

Asia WGS AF: 0.0470 AC: 164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.50
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17126268; hg19: chr1-102726399;