rs229116

Positions:

• chr21-26871278-A-G
• chr21-26871278-A-T
• chr21-26871278-A-C

Variant summary

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

The XR_937632.3(LOC105372760):​n.323+16062A>G 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 0.499 in 152,128 control chromosomes in the GnomAD database, including 19,648 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 0.50 (19648 hom., cov: 33)
• Consequence: LOC105372760 XR_937632.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

LOC105372760 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372760	XR_937632.3	n.323+16062A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75867 AN: 152010 Hom.: 19620 Cov.: 33

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.499 AC: 75948 AN: 152128 Hom.: 19648 Cov.: 33 AF XY: 0.493 AC XY: 36654 AN XY: 74366

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.464

Alfa AF: 0.454 Hom.: 2122

Bravo AF: 0.515

Asia WGS AF: 0.456 AC: 1586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs229116; hg19: chr21-28243597; COSMIC: COSV53892031;