rs10482889

chr21-17667969-C-AchrNT_187627.1-64274-C-Achr21-17667969-C-TchrNT_187627.1-64274-C-T

Variant summary

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

The XR_007067821.1(LOC124904999):n.64+6387G>T 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 0.0934 in 152,152 control chromosomes in the GnomAD database, including 1,888 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 0.093 (1888 hom., cov: 32)
• Consequence: LOC124904999 XR_007067821.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128

Genes affected

LOC124904999 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904999	XR_007067821.1	n.64+6387G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0933 AC: 14179 AN: 152034 Hom.: 1881 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0485

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.0678

Gnomad FIN AF: 0.00302

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.00738

Gnomad OTH AF: 0.0708

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

GnomAD4 genome AF: 0.0934 AC: 14211 AN: 152152 Hom.: 1888 Cov.: 32 AF XY: 0.0918 AC XY: 6831 AN XY: 74414

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.0483

Gnomad4 ASJ AF: 0.0769

Gnomad4 EAS AF: 0.0249

Gnomad4 SAS AF: 0.0666

Gnomad4 FIN AF: 0.00302

Gnomad4 NFE AF: 0.00737

Gnomad4 OTH AF: 0.0767

Alfa AF: 0.0104 Hom.: 14

Bravo AF: 0.105

Asia WGS AF: 0.0690 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.5
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10482889; hg19: chr21-19040287;