1-203523592-C-T

Position:

• chr1-203523592-C-T

Variant summary

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

The XR_007066809.1(LOC124904488):​n.282-8369C>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 0.674 in 152,008 control chromosomes in the GnomAD database, including 34,848 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 0.67 (34848 hom., cov: 31)
• Consequence: LOC124904488 XR_007066809.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303

Genes affected

LOC124904488 (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 (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904488	XR_007066809.1	n.282-8369C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102375 AN: 151890 Hom.: 34795 Cov.: 31

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.674 AC: 102497 AN: 152008 Hom.: 34848 Cov.: 31 AF XY: 0.676 AC XY: 50228 AN XY: 74322

Gnomad4 AFR AF: 0.766

Gnomad4 AMR AF: 0.733

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.645

Alfa AF: 0.652 Hom.: 4016

Bravo AF: 0.687

Asia WGS AF: 0.626 AC: 2178 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	4.4
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13303128; hg19: chr1-203492720; COSMIC: COSV60018510;