chr1-160647267-C-T

Position:

• chr1-160647267-C-T

Variant summary

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

The XR_001738266.2(LOC107985220):​n.259C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0961 in 250,658 control chromosomes in the GnomAD database, including 1,743 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 0.094 (931 hom., cov: 31)
  • Exomes 𝑓: 0.10 (812 hom.)
• Consequence: LOC107985220 XR_001738266.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

Genes affected

LOC107985220 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985220	XR_001738266.2	n.259C>T		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0939 AC: 14270 AN: 152012 Hom.: 929 Cov.: 31

Gnomad AFR AF: 0.0912

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.0965

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0706

Gnomad OTH AF: 0.0920

GnomAD4 exome AF: 0.0995 AC: 9805 AN: 98528 Hom.: 812 Cov.: 0 AF XY: 0.0979 AC XY: 5156 AN XY: 52656

Gnomad4 AFR exome AF: 0.0775

Gnomad4 AMR exome AF: 0.107

Gnomad4 ASJ exome AF: 0.0358

Gnomad4 EAS exome AF: 0.362

Gnomad4 SAS exome AF: 0.0861

Gnomad4 FIN exome AF: 0.128

Gnomad4 NFE exome AF: 0.0744

Gnomad4 OTH exome AF: 0.0859

GnomAD4 genome AF: 0.0939 AC: 14291 AN: 152130 Hom.: 931 Cov.: 31 AF XY: 0.0977 AC XY: 7263 AN XY: 74352

Gnomad4 AFR AF: 0.0914

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0297

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.0966

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.0706

Gnomad4 OTH AF: 0.0944

Alfa AF: 0.0628 Hom.: 346

Bravo AF: 0.0917

Asia WGS AF: 0.192 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.4
DANN	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2295613; hg19: chr1-160617057;