chr1-161493541-G-A

Variant names:

• chr1-161493541-G-A
• rs7511868
• XR_922214.3:n.1825G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

LOC105371473 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.399 AC: 16521 AN: 41420

American (AMR) AF: 0.574 AC: 8766 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1733 AN: 3470

East Asian (EAS) AF: 0.261 AC: 1351 AN: 5182

South Asian (SAS) AF: 0.415 AC: 2000 AN: 4820

European-Finnish (FIN) AF: 0.517 AC: 5450 AN: 10546

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39640 AN: 67954

Other (OTH) AF: 0.526 AC: 1110 AN: 2112

Alfa AF: 0.526 Hom.: 9217

Bravo AF: 0.510

Asia WGS AF: 0.359 AC: 1252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.7
DANN	Benign	0.78
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7511868; hg19: chr1-161463331;