rs1019026

Variant names:

• chr7-13860259-A-T
• rs1019026
• ENST00000654062.1:n.484-1236T>A

Variant summary

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

The ENST00000654062.1(ENSG00000224330):​n.484-1236T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 151,742 control chromosomes in the GnomAD database, including 4,247 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 0.20 (4247 hom., cov: 32)
• Consequence: ENSG00000224330 ENST00000654062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

ENSG00000224330 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 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
ENSG00000224330	ENST00000654062.1	n.484-1236T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30125 AN: 151626 Hom.: 4225 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0474

Gnomad SAS AF: 0.0699

Gnomad FIN AF: 0.0886

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.199 AC: 30201 AN: 151742 Hom.: 4247 Cov.: 32 AF XY: 0.194 AC XY: 14379 AN XY: 74156

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.0473

Gnomad4 SAS AF: 0.0698

Gnomad4 FIN AF: 0.0886

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.188

Alfa AF: 0.167 Hom.: 371

Bravo AF: 0.220

Asia WGS AF: 0.107 AC: 376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1019026; hg19: chr7-13899884; COSMIC: COSV71446853;