22-19733950-C-A

Position:

• chr22-19733950-C-A

Variant summary

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

The XR_938005.3(LOC105372861):​n.1215-737C>A 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 0.435 in 152,066 control chromosomes in the GnomAD database, including 16,838 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 0.44 (16838 hom., cov: 34)
• Consequence: LOC105372861 XR_938005.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.743

Genes affected

LOC105372861 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372861	XR_938005.3	n.1215-737C>A		intron_variant, non_coding_transcript_variant
LOC105372861	XR_007068004.1	n.1780-737C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66092 AN: 151948 Hom.: 16809 Cov.: 34

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.435 AC: 66165 AN: 152066 Hom.: 16838 Cov.: 34 AF XY: 0.442 AC XY: 32852 AN XY: 74342

Gnomad4 AFR AF: 0.685

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.398

Alfa AF: 0.345 Hom.: 2491

Bravo AF: 0.456

Asia WGS AF: 0.517 AC: 1795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.73
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5748411; hg19: chr22-19721473; COSMIC: COSV68315055;