chr22-24005875-G-A

Variant names:

• chr22-24005875-G-A
• rs5760176
• XR_001755457.1:n.200G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The XR_001755457.1(LOC105372959):​n.200G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.37 (769 hom., cov: 35)
  • Failed GnomAD Quality Control
• Consequence: LOC105372959 XR_001755457.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 28 publications found

Genes affected

LOC105372959 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372959	XR_001755457.1	n.200G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298726	ENST00000757608.1	n.130+60G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.371 AC: 47913 AN: 129072 Hom.: 768 Cov.: 35

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.379

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.371 AC: 47920 AN: 129144 Hom.: 769 Cov.: 35 AF XY: 0.373 AC XY: 23661 AN XY: 63420

African (AFR) AF: 0.244 AC: 6281 AN: 25766

American (AMR) AF: 0.398 AC: 5333 AN: 13414

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1238 AN: 3316

East Asian (EAS) AF: 0.263 AC: 1214 AN: 4618

South Asian (SAS) AF: 0.422 AC: 1954 AN: 4628

European-Finnish (FIN) AF: 0.429 AC: 4276 AN: 9974

Middle Eastern (MID) AF: 0.398 AC: 98 AN: 246

European-Non Finnish (NFE) AF: 0.410 AC: 26458 AN: 64476

Other (OTH) AF: 0.378 AC: 700 AN: 1854

Alfa AF: 0.419 Hom.: 7295

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.5
DANN	Benign	0.74
PhyloP100		0.065
PromoterAI		0.015	Neutral

Splicing

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

Other links and lift over

dbSNP: rs5760176; hg19: chr22-24402321;