1-208680564-C-T

Position:

• chr1-208680564-C-T

Variant summary

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

The XR_007066854.1(LOC105372892):​n.215+313G>A 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 0.0155 in 152,282 control chromosomes in the GnomAD database, including 135 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 0.015 (135 hom., cov: 32)
• Consequence: LOC105372892 XR_007066854.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754

Genes affected

LOC105372892 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372892	XR_007066854.1	n.215+313G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0155 AC: 2363 AN: 152164 Hom.: 135 Cov.: 32

Gnomad AFR AF: 0.00169

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0286

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.00641

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00200

Gnomad OTH AF: 0.0139

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

GnomAD4 genome AF: 0.0155 AC: 2359 AN: 152282 Hom.: 135 Cov.: 32 AF XY: 0.0185 AC XY: 1380 AN XY: 74466

Gnomad4 AFR AF: 0.00166

Gnomad4 AMR AF: 0.0285

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.00641

Gnomad4 NFE AF: 0.00200

Gnomad4 OTH AF: 0.0147

Alfa AF: 0.00340 Hom.: 3

Bravo AF: 0.0161

Asia WGS AF: 0.154 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494903; hg19: chr1-208853909;