rs1021055

Variant names:

• chr10-44577763-G-A
• rs1021055
• XR_007062357.1:n.562G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-44577763-G-A
• chr10-44577763-G-C

Variant summary

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

The XR_007062357.1(LOC124902533):​n.562G>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 0.411 in 152,010 control chromosomes in the GnomAD database, including 13,926 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 0.41 (13926 hom., cov: 32)
• Consequence: LOC124902533 XR_007062357.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372
• Publications: 4 publications found

Genes affected

LOC124902533 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902533	XR_007062357.1	n.562G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62439 AN: 151892 Hom.: 13910 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.411 AC: 62495 AN: 152010 Hom.: 13926 Cov.: 32 AF XY: 0.415 AC XY: 30820 AN XY: 74276

African (AFR) AF: 0.233 AC: 9660 AN: 41480

American (AMR) AF: 0.490 AC: 7479 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1353 AN: 3462

East Asian (EAS) AF: 0.447 AC: 2308 AN: 5158

South Asian (SAS) AF: 0.511 AC: 2457 AN: 4810

European-Finnish (FIN) AF: 0.502 AC: 5289 AN: 10534

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32446 AN: 67976

Other (OTH) AF: 0.422 AC: 891 AN: 2112

Alfa AF: 0.451 Hom.: 9327

Bravo AF: 0.405

Asia WGS AF: 0.493 AC: 1716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.26
DANN	Benign	0.33
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs1021055; hg19: chr10-45073211;