XR_007066779.1:n.257+834G>A

Variant names:

• chr1-196932623-C-T
• rs7538501
• XR_007066779.1:n.257+834G>A

Variant summary

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

The XR_007066779.1(LOC105371675):​n.257+834G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 151,522 control chromosomes in the GnomAD database, including 2,881 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 0.17 (2881 hom., cov: 32)
• Consequence: LOC105371675 XR_007066779.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• Publications: 7 publications found

Genes affected

LOC105371675 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25363 AN: 151404 Hom.: 2878 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0928

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.167 AC: 25376 AN: 151522 Hom.: 2881 Cov.: 32 AF XY: 0.165 AC XY: 12233 AN XY: 74074

African (AFR) AF: 0.285 AC: 11693 AN: 41032

American (AMR) AF: 0.127 AC: 1927 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 403 AN: 3466

East Asian (EAS) AF: 0.000774 AC: 4 AN: 5168

South Asian (SAS) AF: 0.145 AC: 697 AN: 4822

European-Finnish (FIN) AF: 0.0928 AC: 981 AN: 10572

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9147 AN: 67948

Other (OTH) AF: 0.178 AC: 375 AN: 2108

Alfa AF: 0.139 Hom.: 1192

Bravo AF: 0.174

Asia WGS AF: 0.0790 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.5
DANN	Benign	0.19
PhyloP100		0.20
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7538501; hg19: chr1-196901753;