chr1-161492938-A-G

Variant names:

• chr1-161492938-A-G
• rs4657039
• XR_922214.3:n.1739-517A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_922214.3(LOC105371473):​n.1739-517A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,904 control chromosomes in the GnomAD database, including 20,451 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 (20451 hom., cov: 31)
• Consequence: LOC105371473 XR_922214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320
• Publications: 16 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=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.583 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: 0.509 AC: 77257 AN: 151786 Hom.: 20452 Cov.: 31

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.509 AC: 77296 AN: 151904 Hom.: 20451 Cov.: 31 AF XY: 0.503 AC XY: 37355 AN XY: 74212

African (AFR) AF: 0.393 AC: 16274 AN: 41420

American (AMR) AF: 0.578 AC: 8812 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1752 AN: 3472

East Asian (EAS) AF: 0.247 AC: 1277 AN: 5162

South Asian (SAS) AF: 0.416 AC: 2001 AN: 4812

European-Finnish (FIN) AF: 0.519 AC: 5462 AN: 10528

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39931 AN: 67948

Other (OTH) AF: 0.528 AC: 1110 AN: 2104

Alfa AF: 0.558 Hom.: 102027

Bravo AF: 0.511

Asia WGS AF: 0.353 AC: 1232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	3.2
DANN	Benign	0.81
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs4657039; hg19: chr1-161462728;