22-19729797-G-A

Variant names:

• chr22-19729797-G-A
• rs4819835
• XR_007068004.1:n.469G>A

Variant summary

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

The XR_007068004.1(LOC105372861):​n.469G>A 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 0.349 in 151,956 control chromosomes in the GnomAD database, including 9,478 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 0.35 (9478 hom., cov: 33)
• Consequence: LOC105372861 XR_007068004.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

LOC105372861 (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 (AMR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372861	XR_007068004.1	n.469G>A		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105372861	XR_938005.3	n.980+1097G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298759	ENST00000757762.1	n.83+2466G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53040 AN: 151836 Hom.: 9458 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.349 AC: 53107 AN: 151956 Hom.: 9478 Cov.: 33 AF XY: 0.352 AC XY: 26127 AN XY: 74288

African (AFR) AF: 0.324 AC: 13428 AN: 41434

American (AMR) AF: 0.451 AC: 6890 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 852 AN: 3472

East Asian (EAS) AF: 0.376 AC: 1936 AN: 5150

South Asian (SAS) AF: 0.228 AC: 1096 AN: 4816

European-Finnish (FIN) AF: 0.401 AC: 4236 AN: 10576

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.350 AC: 23741 AN: 67920

Other (OTH) AF: 0.332 AC: 702 AN: 2114

Alfa AF: 0.340 Hom.: 14022

Bravo AF: 0.356

Asia WGS AF: 0.320 AC: 1112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.77
PhyloP100		-1.0

Splicing

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

Publications

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Other links and lift over

dbSNP: rs4819835; hg19: chr22-19717320;