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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984191	XR_007062029.1	n.559G>A		non_coding_transcript_exon_variant	Exon 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;