rs8125625

chr20-55811889-T-C

Variant summary

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

The XR_936887.2(LOC105372677):n.83+7907T>C 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 0.329 in 152,002 control chromosomes in the GnomAD database, including 11,457 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 0.33 (11457 hom., cov: 32)
• Consequence: LOC105372677 XR_936887.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219

Genes affected

LOC105372677 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372677	XR_936887.2	n.83+7907T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49891 AN: 151884 Hom.: 11426 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.329 AC: 49969 AN: 152002 Hom.: 11457 Cov.: 32 AF XY: 0.324 AC XY: 24050 AN XY: 74304

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.302

Alfa AF: 0.217 Hom.: 8105

Bravo AF: 0.342

Asia WGS AF: 0.212 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.9
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8125625; hg19: chr20-54386945;