1-19292107-C-T

Variant names:

• chr1-19292107-C-T
• rs9729157
• XR_007065521.1:n.301+3747C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007065521.1(LOC124903867):​n.301+3747C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.631 in 151,834 control chromosomes in the GnomAD database, including 30,406 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 0.63 (30406 hom., cov: 30)
• Consequence: LOC124903867 XR_007065521.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 11 publications found

Genes affected

LOC124903867 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.709 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: 0.631 AC: 95804 AN: 151718 Hom.: 30387 Cov.: 30

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.631 AC: 95862 AN: 151834 Hom.: 30406 Cov.: 30 AF XY: 0.636 AC XY: 47180 AN XY: 74214

African (AFR) AF: 0.565 AC: 23361 AN: 41378

American (AMR) AF: 0.720 AC: 10994 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2280 AN: 3472

East Asian (EAS) AF: 0.672 AC: 3465 AN: 5160

South Asian (SAS) AF: 0.634 AC: 3053 AN: 4818

European-Finnish (FIN) AF: 0.674 AC: 7081 AN: 10504

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.640 AC: 43498 AN: 67924

Other (OTH) AF: 0.654 AC: 1382 AN: 2114

Alfa AF: 0.643 Hom.: 50696

Bravo AF: 0.633

Asia WGS AF: 0.651 AC: 2261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.7
DANN	Benign	0.80
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs9729157; hg19: chr1-19618601;