XR_007066779.1:n.257+4762G>A

Variant names:

• chr1-196928695-C-T
• rs9427642
• XR_007066779.1:n.257+4762G>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+4762G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.15 (554 hom., cov: 9)
• Consequence: LOC105371675 XR_007066779.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 1 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 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: 0.145 AC: 10031 AN: 69010 Hom.: 555 Cov.: 9

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0517

Gnomad SAS AF: 0.0967

Gnomad FIN AF: 0.0706

Gnomad MID AF: 0.0603

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.145 AC: 10032 AN: 69000 Hom.: 554 Cov.: 9 AF XY: 0.143 AC XY: 4586 AN XY: 32096

African (AFR) AF: 0.221 AC: 2839 AN: 12822

American (AMR) AF: 0.198 AC: 1251 AN: 6326

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 191 AN: 1772

East Asian (EAS) AF: 0.0518 AC: 85 AN: 1640

South Asian (SAS) AF: 0.0967 AC: 183 AN: 1892

European-Finnish (FIN) AF: 0.0706 AC: 221 AN: 3132

Middle Eastern (MID) AF: 0.0588 AC: 6 AN: 102

European-Non Finnish (NFE) AF: 0.128 AC: 5085 AN: 39788

Other (OTH) AF: 0.142 AC: 135 AN: 950

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.070
PhyloP100		0.0
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: rs9427642; hg19: chr1-196897825;