10-271561-C-T

Variant names:

• chr10-271561-C-T
• rs2018975
• XR_007062029.1:n.559G>A

Variant summary

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

The XR_007062029.1(LOC107984191):​n.559G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,030 control chromosomes in the GnomAD database, including 8,344 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 0.32 (8344 hom., cov: 32)
• Consequence: LOC107984191 XR_007062029.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 5 publications found

Genes affected

LOC107984191 (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 (EAS) allele frequency at 95% confidence interval = 0.501 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: 0.325 AC: 49338 AN: 151912 Hom.: 8322 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.325 AC: 49401 AN: 152030 Hom.: 8344 Cov.: 32 AF XY: 0.331 AC XY: 24565 AN XY: 74322

African (AFR) AF: 0.297 AC: 12310 AN: 41484

American (AMR) AF: 0.378 AC: 5768 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1146 AN: 3470

East Asian (EAS) AF: 0.518 AC: 2677 AN: 5170

South Asian (SAS) AF: 0.365 AC: 1752 AN: 4798

European-Finnish (FIN) AF: 0.402 AC: 4247 AN: 10562

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20599 AN: 67964

Other (OTH) AF: 0.312 AC: 657 AN: 2104

Alfa AF: 0.314 Hom.: 30487

Bravo AF: 0.328

Asia WGS AF: 0.404 AC: 1404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.66
DANN	Benign	0.42
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs2018975; hg19: chr10-317501;