chr1-209062987-T-A

Variant names:

• chr1-209062987-T-A
• rs17014011
• XR_001738441.2:n.495+69767A>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_001738441.2(LOC107985255):​n.495+69767A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,246 control chromosomes in the GnomAD database, including 1,363 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 (1363 hom., cov: 33)
• Consequence: LOC107985255 XR_001738441.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.946
• Publications: 2 publications found

Genes affected

LOC107985255 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19802 AN: 152128 Hom.: 1358 Cov.: 33

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0916

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.130 AC: 19829 AN: 152246 Hom.: 1363 Cov.: 33 AF XY: 0.128 AC XY: 9508 AN XY: 74444

African (AFR) AF: 0.136 AC: 5672 AN: 41556

American (AMR) AF: 0.115 AC: 1758 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 609 AN: 3472

East Asian (EAS) AF: 0.115 AC: 595 AN: 5172

South Asian (SAS) AF: 0.0929 AC: 449 AN: 4832

European-Finnish (FIN) AF: 0.107 AC: 1139 AN: 10596

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9208 AN: 68008

Other (OTH) AF: 0.131 AC: 277 AN: 2108

Alfa AF: 0.136 Hom.: 199

Bravo AF: 0.132

Asia WGS AF: 0.112 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	18
DANN	Benign	0.85
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs17014011; hg19: chr1-209236332; COSMIC: COSV60021131;