rs6513195

Variant names:

• chr20-56151513-G-A
• rs6513195
• XR_001754685.2:n.1074-8927C>T

Variant summary

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

The XR_936893.3(LOC105372680):​n.983-8927C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,086 control chromosomes in the GnomAD database, including 7,928 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 0.30 (7928 hom., cov: 32)
• Consequence: LOC105372680 XR_936893.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151
• Publications: 4 publications found

Genes affected

LOC105372680 (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 (AFR) allele frequency at 95% confidence interval = 0.483 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: 0.299 AC: 45427 AN: 151968 Hom.: 7902 Cov.: 32

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.299 AC: 45502 AN: 152086 Hom.: 7928 Cov.: 32 AF XY: 0.296 AC XY: 22015 AN XY: 74344

African (AFR) AF: 0.489 AC: 20260 AN: 41456

American (AMR) AF: 0.205 AC: 3130 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 582 AN: 3466

East Asian (EAS) AF: 0.383 AC: 1978 AN: 5164

South Asian (SAS) AF: 0.253 AC: 1219 AN: 4816

European-Finnish (FIN) AF: 0.268 AC: 2831 AN: 10582

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14741 AN: 67994

Other (OTH) AF: 0.256 AC: 541 AN: 2116

Alfa AF: 0.238 Hom.: 2753

Bravo AF: 0.303

Asia WGS AF: 0.366 AC: 1275 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	7.6
DANN	Benign	0.77
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs6513195; hg19: chr20-54726569;