chr1-193520039-C-T

Position:

• chr1-193520039-C-T

Variant summary

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

The ENST00000656143.1(ENSG00000227240):​n.153+46663C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 151,992 control chromosomes in the GnomAD database, including 27,640 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 0.59 (27640 hom., cov: 31)
• Consequence: ENSG00000227240 ENST00000656143.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

Genes affected

ENSG00000227240 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904475	XR_007066777.1	n.5234+46663C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000227240	ENST00000656143.1	n.153+46663C>T		intron_variant
ENSG00000288950	ENST00000691564.1	n.253-26009C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90201 AN: 151874 Hom.: 27613 Cov.: 31

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.594 AC: 90271 AN: 151992 Hom.: 27640 Cov.: 31 AF XY: 0.588 AC XY: 43662 AN XY: 74264

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.593

Alfa AF: 0.588 Hom.: 10745

Bravo AF: 0.581

Asia WGS AF: 0.358 AC: 1244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.078
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7554157; hg19: chr1-193489169;