chr1-100705443-C-T

Variant names:

• chr1-100705443-C-T
• rs11578560
• XR_007066256.1:n.1719C>T

Variant summary

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

The XR_007066256.1(LOC124904231):​n.1719C>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 0.132 in 151,906 control chromosomes in the GnomAD database, including 1,789 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 0.13 (1789 hom., cov: 32)
• Consequence: LOC124904231 XR_007066256.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

Genes affected

LOC124904231 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904231	XR_007066256.1	n.1719C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20001 AN: 151788 Hom.: 1785 Cov.: 32

Gnomad AFR AF: 0.0395

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.132 AC: 20002 AN: 151906 Hom.: 1789 Cov.: 32 AF XY: 0.133 AC XY: 9895 AN XY: 74230

Gnomad4 AFR AF: 0.0394

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.185

Alfa AF: 0.151 Hom.: 424

Bravo AF: 0.140

Asia WGS AF: 0.131 AC: 455 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.4
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11578560; hg19: chr1-101170999;