rs10446073

chr21-17820455-G-T

Variant summary

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

The XR_007067823.1(LOC124900465):n.1605+63666G>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 0.0642 in 152,208 control chromosomes in the GnomAD database, including 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 0.064 (344 hom., cov: 32)
• Consequence: LOC124900465 XR_007067823.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

Genes affected

LOC124900465 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900465	XR_007067823.1	n.1605+63666G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0640 AC: 9733 AN: 152090 Hom.: 344 Cov.: 32

Gnomad AFR AF: 0.0853

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0523

Gnomad ASJ AF: 0.0407

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.0564

Gnomad FIN AF: 0.0603

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.0564

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

GnomAD4 genome AF: 0.0642 AC: 9766 AN: 152208 Hom.: 344 Cov.: 32 AF XY: 0.0643 AC XY: 4788 AN XY: 74410

Gnomad4 AFR AF: 0.0856

Gnomad4 AMR AF: 0.0528

Gnomad4 ASJ AF: 0.0407

Gnomad4 EAS AF: 0.0307

Gnomad4 SAS AF: 0.0564

Gnomad4 FIN AF: 0.0603

Gnomad4 NFE AF: 0.0597

Gnomad4 OTH AF: 0.0572

Alfa AF: 0.0589 Hom.: 413

Bravo AF: 0.0646

Asia WGS AF: 0.0720 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	3.0
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10446073; hg19: chr21-19192772;