rs6129969

chr20-41905933-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001754611.2(LOC101927182):n.252+1834C>T variant causes a intron, non coding transcript 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_001754611.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

Genes affected

LOC101927182 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927182	XR_001754611.2	n.252+1834C>T		intron_variant, non_coding_transcript_variant
LOC101927182	XR_001754609.2	n.247+1838C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.0851

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.134

Alfa AF: 0.127 Hom.: 178

Bravo AF: 0.148

Asia WGS AF: 0.292 AC: 1014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	4.5
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6129969; hg19: chr20-40534573;