rs1019026

Positions:

• chr7-13860259-A-T

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, non coding transcript 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: ENST00000654062.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654062.1	n.484-1236T>A		intron_variant, non_coding_transcript_variant

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;