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_001754685.2(LOC105372680):​n.1074-8927C>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_001754685.2 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372680	XR_001754685.2	n.1074-8927C>T		intron_variant	Intron 2 of 2
LOC105372680	XR_936893.3	n.983-8927C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;