rs7511868

chr1-161493541-G-A

Variant summary

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

The XR_922214.3(LOC105371473):n.1825G>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 0.508 in 151,984 control chromosomes in the GnomAD database, including 20,334 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 0.51 (20334 hom., cov: 32)
• Consequence: LOC105371473 XR_922214.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

LOC105371473 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371473	XR_922214.3	n.1825G>A		non_coding_transcript_exon_variant	2/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77201 AN: 151866 Hom.: 20331 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.508 AC: 77242 AN: 151984 Hom.: 20334 Cov.: 32 AF XY: 0.503 AC XY: 37349 AN XY: 74282

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.526

Alfa AF: 0.538 Hom.: 5795

Bravo AF: 0.510

Asia WGS AF: 0.359 AC: 1252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	1.7
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7511868; hg19: chr1-161463331;