20-55811889-T-C

Variant names:

• chr20-55811889-T-C
• rs8125625
• XR_936887.2:n.83+7907T>C

Variant summary

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

The XR_936887.2(LOC105372677):​n.83+7907T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219

Genes affected

LOC105372677 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105372677	XR_936887.2	n.83+7907T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.658 AC: 27294 AN: 41450

American (AMR) AF: 0.207 AC: 3161 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1056 AN: 3470

East Asian (EAS) AF: 0.138 AC: 711 AN: 5170

South Asian (SAS) AF: 0.230 AC: 1112 AN: 4826

European-Finnish (FIN) AF: 0.201 AC: 2129 AN: 10594

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13602 AN: 67938

Other (OTH) AF: 0.302 AC: 637 AN: 2112

Alfa AF: 0.245 Hom.: 18196

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
PhyloP100		0.22

Splicing

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

Publications

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Other links and lift over

dbSNP: rs8125625; hg19: chr20-54386945;