rs6129969

Variant names:

• chr20-41905933-C-T
• rs6129969
• XR_001754609.2:n.247+1838C>T

Variant summary

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

The XR_001754609.2(LOC101927182):​n.247+1838C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,076 control chromosomes in the GnomAD database, including 1,733 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 0.14 (1733 hom., cov: 32)
• Consequence: LOC101927182 XR_001754609.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 3 publications found

Genes affected

LOC101927182 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.339 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: 0.142 AC: 21565 AN: 151958 Hom.: 1722 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0851

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.142 AC: 21611 AN: 152076 Hom.: 1733 Cov.: 32 AF XY: 0.147 AC XY: 10902 AN XY: 74332

African (AFR) AF: 0.176 AC: 7308 AN: 41456

American (AMR) AF: 0.151 AC: 2312 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0851 AC: 295 AN: 3468

East Asian (EAS) AF: 0.353 AC: 1828 AN: 5182

South Asian (SAS) AF: 0.255 AC: 1225 AN: 4804

European-Finnish (FIN) AF: 0.108 AC: 1140 AN: 10574

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7043 AN: 68002

Other (OTH) AF: 0.134 AC: 283 AN: 2112

Alfa AF: 0.128 Hom.: 190

Bravo AF: 0.148

Asia WGS AF: 0.292 AC: 1014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	4.5
DANN	Benign	0.53
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs6129969; hg19: chr20-40534573;