rs4915318

Variant names:

• chr1-196927958-C-A
• rs4915318
• XR_007066779.1:n.258-4947G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-196927958-C-A
• chr1-196927958-C-G
• chr1-196927958-C-T

Variant summary

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

The XR_007066779.1(LOC105371675):​n.258-4947G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 150,974 control chromosomes in the GnomAD database, including 5,935 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 0.24 (5935 hom., cov: 31)
• Consequence: LOC105371675 XR_007066779.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199
• Publications: 12 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 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: 0.235 AC: 35508 AN: 150862 Hom.: 5926 Cov.: 31

Gnomad AFR AF: 0.0776

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.235 AC: 35525 AN: 150974 Hom.: 5935 Cov.: 31 AF XY: 0.246 AC XY: 18141 AN XY: 73756

African (AFR) AF: 0.0776 AC: 3176 AN: 40932

American (AMR) AF: 0.391 AC: 5904 AN: 15112

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1066 AN: 3466

East Asian (EAS) AF: 0.721 AC: 3676 AN: 5098

South Asian (SAS) AF: 0.331 AC: 1591 AN: 4802

European-Finnish (FIN) AF: 0.305 AC: 3204 AN: 10510

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.239 AC: 16192 AN: 67748

Other (OTH) AF: 0.256 AC: 538 AN: 2102

Alfa AF: 0.199 Hom.: 1260

Bravo AF: 0.240

Asia WGS AF: 0.507 AC: 1760 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.13
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: rs4915318; hg19: chr1-196897088;