XR_947651.2:n.159-100A>G

Variant names:

• chr1-102648125-T-C
• rs977155
• XR_947651.2:n.159-100A>G

Variant summary

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

The XR_947651.2(LOC105378874):​n.159-100A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 151,996 control chromosomes in the GnomAD database, including 20,854 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 (20854 hom., cov: 32)
• Consequence: LOC105378874 XR_947651.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462
• Publications: 3 publications found

Genes affected

LOC105378874 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75483 AN: 151878 Hom.: 20838 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.497 AC: 75511 AN: 151996 Hom.: 20854 Cov.: 32 AF XY: 0.506 AC XY: 37548 AN XY: 74274

African (AFR) AF: 0.237 AC: 9837 AN: 41494

American (AMR) AF: 0.624 AC: 9521 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1756 AN: 3472

East Asian (EAS) AF: 0.604 AC: 3110 AN: 5152

South Asian (SAS) AF: 0.557 AC: 2686 AN: 4818

European-Finnish (FIN) AF: 0.703 AC: 7421 AN: 10554

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39439 AN: 67940

Other (OTH) AF: 0.501 AC: 1058 AN: 2112

Alfa AF: 0.408 Hom.: 1274

Bravo AF: 0.483

Asia WGS AF: 0.582 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.48
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs977155; hg19: chr1-103113681;