22-38904931-A-G

Position:

• chr22-38904931-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_938256.2(LOC105373032):​n.722-16245A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 152,148 control chromosomes in the GnomAD database, including 39,531 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 0.71 (39531 hom., cov: 32)
• Consequence: LOC105373032 XR_938256.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.89

Genes affected

LOC105373032 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373032	XR_938256.2	n.722-16245A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107186 AN: 152030 Hom.: 39482 Cov.: 32

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.705 AC: 107283 AN: 152148 Hom.: 39531 Cov.: 32 AF XY: 0.702 AC XY: 52207 AN XY: 74382

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.677

Alfa AF: 0.646 Hom.: 14686

Bravo AF: 0.705

Asia WGS AF: 0.745 AC: 2594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2413552; hg19: chr22-39300936;