chr2-193075795-A-G

Variant names:

• chr2-193075795-A-G
• rs1840947
• XR_001739832.2:n.234-25364T>C

Variant summary

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

The XR_001739832.2(LOC107985969):​n.234-25364T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,806 control chromosomes in the GnomAD database, including 18,314 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 0.49 (18314 hom., cov: 32)
• Consequence: LOC107985969 XR_001739832.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 2 publications found

Genes affected

LOC107985969 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 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: 0.487 AC: 73933 AN: 151690 Hom.: 18287 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.488 AC: 74009 AN: 151806 Hom.: 18314 Cov.: 32 AF XY: 0.488 AC XY: 36180 AN XY: 74174

African (AFR) AF: 0.401 AC: 16583 AN: 41376

American (AMR) AF: 0.548 AC: 8346 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1536 AN: 3468

East Asian (EAS) AF: 0.569 AC: 2931 AN: 5154

South Asian (SAS) AF: 0.395 AC: 1905 AN: 4820

European-Finnish (FIN) AF: 0.515 AC: 5440 AN: 10556

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35676 AN: 67888

Other (OTH) AF: 0.462 AC: 974 AN: 2110

Alfa AF: 0.502 Hom.: 2921

Bravo AF: 0.494

Asia WGS AF: 0.454 AC: 1581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.54
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs1840947; hg19: chr2-193940521; COSMIC: COSV56532665;