1-204573452-T-C

Variant summary

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

The XR_007066814.1(LOC105371692):n.1204-235T>C 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 0.561 in 152,112 control chromosomes in the GnomAD database, including 26,602 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 0.56 (26602 hom., cov: 32)
• Consequence: LOC105371692 XR_007066814.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.410

Genes affected

LOC105371692 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371692	XR_007066814.1	n.1204-235T>C		intron_variant, non_coding_transcript_variant
LOC105371692	XR_007066816.1	n.2425T>C		non_coding_transcript_exon_variant	1/12
LOC105371692	XR_007066815.1	n.131-235T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85263 AN: 151994 Hom.: 26601 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.561 AC: 85271 AN: 152112 Hom.: 26602 Cov.: 32 AF XY: 0.567 AC XY: 42190 AN XY: 74352

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.680

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.565

Alfa AF: 0.643 Hom.: 9043

Bravo AF: 0.533

Asia WGS AF: 0.587 AC: 2042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	9.4
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12039454; hg19: chr1-204542580;