rs6691481

Variant names:

• chr1-19017385-A-G
• rs6691481
• XR_947015.2:n.552-20326T>C

Variant summary

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

The XR_947015.2(LOC105376815):​n.552-20326T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,126 control chromosomes in the GnomAD database, including 8,463 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 0.29 (8463 hom., cov: 32)
• Consequence: LOC105376815 XR_947015.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• Publications: 2 publications found

Genes affected

LOC105376815 (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 = 0.534 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: 0.288 AC: 43847 AN: 152008 Hom.: 8452 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.00288

Gnomad SAS AF: 0.0869

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.289 AC: 43898 AN: 152126 Hom.: 8463 Cov.: 32 AF XY: 0.279 AC XY: 20737 AN XY: 74370

African (AFR) AF: 0.540 AC: 22385 AN: 41434

American (AMR) AF: 0.248 AC: 3793 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3472

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5194

South Asian (SAS) AF: 0.0865 AC: 417 AN: 4820

European-Finnish (FIN) AF: 0.109 AC: 1155 AN: 10590

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14421 AN: 68006

Other (OTH) AF: 0.271 AC: 572 AN: 2114

Alfa AF: 0.225 Hom.: 2245

Bravo AF: 0.312

Asia WGS AF: 0.0770 AC: 271 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	3.7
DANN	Benign	0.32
PhyloP100		-0.074

Splicing

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

Other links and lift over

dbSNP: rs6691481; hg19: chr1-19343879;