rs1547374

Positions:

• chr21-42358786-A-G
• chr21-42358786-A-T

Variant summary

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

The XR_937755.3(LOC105372815):​n.1022A>G 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 0.323 in 152,004 control chromosomes in the GnomAD database, including 8,165 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 (8165 hom., cov: 32)
• Consequence: LOC105372815 XR_937755.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.749

Genes affected

LOC105372815 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372815	XR_007067875.1	n.1022A>G		non_coding_transcript_exon_variant	2/4
LOC105372815	XR_007067876.1	n.880A>G		non_coding_transcript_exon_variant	3/4
LOC105372815	XR_007067877.1	n.314A>G		non_coding_transcript_exon_variant	3/4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49030 AN: 151886 Hom.: 8143 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.323 AC: 49104 AN: 152004 Hom.: 8165 Cov.: 32 AF XY: 0.322 AC XY: 23894 AN XY: 74298

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.353

Alfa AF: 0.321 Hom.: 17615

Bravo AF: 0.334

Asia WGS AF: 0.379 AC: 1317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1547374; hg19: chr21-43778895;