chr2-138061031-T-C

Variant names:

• chr2-138061031-T-C
• rs1996872
• XR_923366.2:n.804A>G

Variant summary

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

The XR_923366.2(LOC105373636):​n.804A>G 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 0.594 in 151,980 control chromosomes in the GnomAD database, including 26,833 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 0.59 (26833 hom., cov: 32)
• Consequence: LOC105373636 XR_923366.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191
• Publications: 5 publications found

Genes affected

LOC105373636 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 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: 0.593 AC: 90121 AN: 151862 Hom.: 26805 Cov.: 32

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.594 AC: 90203 AN: 151980 Hom.: 26833 Cov.: 32 AF XY: 0.592 AC XY: 43950 AN XY: 74296

African (AFR) AF: 0.623 AC: 25836 AN: 41470

American (AMR) AF: 0.611 AC: 9319 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2334 AN: 3464

East Asian (EAS) AF: 0.454 AC: 2342 AN: 5156

South Asian (SAS) AF: 0.589 AC: 2832 AN: 4810

European-Finnish (FIN) AF: 0.558 AC: 5882 AN: 10548

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39647 AN: 67954

Other (OTH) AF: 0.608 AC: 1282 AN: 2108

Alfa AF: 0.591 Hom.: 4605

Bravo AF: 0.600

Asia WGS AF: 0.572 AC: 1987 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.2
DANN	Benign	0.57
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1996872; hg19: chr2-138818601;