rs526593

Positions:

• chr1-194128586-A-T

Variant summary

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

The ENST00000656143.1(ENSG00000227240):​n.379-68937A>T 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 0.317 in 151,986 control chromosomes in the GnomAD database, including 12,732 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 0.32 (12732 hom., cov: 33)
• Consequence: ENST00000656143.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904475	XR_007066777.1	n.5458+2401A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000656143.1	n.379-68937A>T		intron_variant, non_coding_transcript_variant
	ENST00000655677.1	n.46+2401A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48104 AN: 151868 Hom.: 12690 Cov.: 33

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.317 AC: 48213 AN: 151986 Hom.: 12732 Cov.: 33 AF XY: 0.314 AC XY: 23336 AN XY: 74298

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.261

Alfa AF: 0.254 Hom.: 1061

Bravo AF: 0.332

Asia WGS AF: 0.209 AC: 728 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs526593; hg19: chr1-194097716; COSMIC: COSV60006795;