1-193588693-C-T

Position:

• chr1-193588693-C-T

Variant summary

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

The ENST00000656143.1(ENSG00000227240):​n.154-84517C>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 0.624 in 151,978 control chromosomes in the GnomAD database, including 29,980 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 0.62 (29980 hom., cov: 31)
• Consequence: ENST00000656143.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.356

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904475	XR_007066777.1	n.5234+115317C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000656143.1	n.154-84517C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94739 AN: 151858 Hom.: 29939 Cov.: 31

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.624 AC: 94837 AN: 151978 Hom.: 29980 Cov.: 31 AF XY: 0.622 AC XY: 46192 AN XY: 74266

Gnomad4 AFR AF: 0.712

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.635

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.632

Alfa AF: 0.594 Hom.: 14705

Bravo AF: 0.633

Asia WGS AF: 0.679 AC: 2362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs913478; hg19: chr1-193557823;