chr1-34627992-G-T

Variant names:

• chr1-34627992-G-T
• rs2093880
• XR_001737964.2:n.156-12297C>A

Variant summary

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

The XR_001737964.2(LOC105378641):​n.156-12297C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0981 in 152,170 control chromosomes in the GnomAD database, including 967 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 0.098 (967 hom., cov: 32)
• Consequence: LOC105378641 XR_001737964.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 3 publications found

Genes affected

LOC105378641 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.18 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: 0.0980 AC: 14907 AN: 152052 Hom.: 960 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.0694

Gnomad AMR AF: 0.0634

Gnomad ASJ AF: 0.0853

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.0920

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.0537

Gnomad OTH AF: 0.0848

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

GnomAD4 genome AF: 0.0981 AC: 14928 AN: 152170 Hom.: 967 Cov.: 32 AF XY: 0.101 AC XY: 7484 AN XY: 74398

African (AFR) AF: 0.166 AC: 6880 AN: 41490

American (AMR) AF: 0.0633 AC: 968 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0853 AC: 296 AN: 3470

East Asian (EAS) AF: 0.190 AC: 982 AN: 5166

South Asian (SAS) AF: 0.187 AC: 900 AN: 4816

European-Finnish (FIN) AF: 0.0920 AC: 976 AN: 10610

Middle Eastern (MID) AF: 0.0651 AC: 19 AN: 292

European-Non Finnish (NFE) AF: 0.0536 AC: 3647 AN: 68016

Other (OTH) AF: 0.0934 AC: 197 AN: 2110

Alfa AF: 0.0693 Hom.: 2106

Bravo AF: 0.0975

Asia WGS AF: 0.229 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.24
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2093880; hg19: chr1-35093593; COSMIC: COSV59937445;