rs2122469

Variant names:

• chr8-20768810-G-A
• rs2122469
• XR_949569.4:n.72-21636G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-20768810-G-A
• chr8-20768810-G-C
• chr8-20768810-G-T

Variant summary

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

The XR_949569.4(LOC105379315):​n.72-21636G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0518 in 152,240 control chromosomes in the GnomAD database, including 235 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 0.052 (235 hom., cov: 32)
• Consequence: LOC105379315 XR_949569.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.344
• Publications: 4 publications found

Genes affected

LOC105379315 (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 (SAS) allele frequency at 95% confidence interval = 0.11 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: 0.0518 AC: 7878 AN: 152122 Hom.: 230 Cov.: 32

Gnomad AFR AF: 0.0383

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0657

Gnomad ASJ AF: 0.0824

Gnomad EAS AF: 0.0669

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0224

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0533

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0518 AC: 7888 AN: 152240 Hom.: 235 Cov.: 32 AF XY: 0.0521 AC XY: 3877 AN XY: 74426

African (AFR) AF: 0.0383 AC: 1590 AN: 41544

American (AMR) AF: 0.0657 AC: 1004 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0824 AC: 286 AN: 3470

East Asian (EAS) AF: 0.0665 AC: 344 AN: 5176

South Asian (SAS) AF: 0.118 AC: 570 AN: 4828

European-Finnish (FIN) AF: 0.0224 AC: 237 AN: 10600

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0533 AC: 3626 AN: 68012

Other (OTH) AF: 0.0620 AC: 131 AN: 2114

Alfa AF: 0.0541 Hom.: 476

Bravo AF: 0.0527

Asia WGS AF: 0.120 AC: 419 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	5.4
DANN	Benign	0.40
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs2122469; hg19: chr8-20626321;