XR_949164.2:n.340+5980A>C

Variant names:

• chr1-223684792-T-G
• rs10495214
• XR_949164.2:n.340+5980A>C

Variant summary

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

The XR_949164.2(LOC105373281):​n.340+5980A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0686 in 152,138 control chromosomes in the GnomAD database, including 775 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 0.069 (775 hom., cov: 32)
• Consequence: LOC105373281 XR_949164.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.985
• Publications: 2 publications found

Genes affected

LOC105373281 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.167 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: 0.0684 AC: 10405 AN: 152020 Hom.: 768 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0782

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.0383

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.00828

Gnomad FIN AF: 0.0157

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0118

Gnomad OTH AF: 0.0731

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

GnomAD4 genome AF: 0.0686 AC: 10435 AN: 152138 Hom.: 775 Cov.: 32 AF XY: 0.0706 AC XY: 5252 AN XY: 74396

African (AFR) AF: 0.134 AC: 5556 AN: 41484

American (AMR) AF: 0.173 AC: 2639 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0383 AC: 133 AN: 3472

East Asian (EAS) AF: 0.167 AC: 862 AN: 5172

South Asian (SAS) AF: 0.00787 AC: 38 AN: 4826

European-Finnish (FIN) AF: 0.0157 AC: 167 AN: 10604

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0118 AC: 802 AN: 67998

Other (OTH) AF: 0.0747 AC: 158 AN: 2114

Alfa AF: 0.0339 Hom.: 1090

Bravo AF: 0.0888

Asia WGS AF: 0.0970 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.90
DANN	Benign	0.44
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs10495214; hg19: chr1-223872494;