rs5748410

chr22-19730621-G-A

Variant summary

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

The XR_938005.3(LOC105372861):n.981-1822G>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 0.658 in 152,152 control chromosomes in the GnomAD database, including 33,512 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 0.66 (33512 hom., cov: 34)
• Consequence: LOC105372861 XR_938005.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17

Genes affected

LOC105372861 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372861	XR_938005.3	n.981-1822G>A		intron_variant, non_coding_transcript_variant
LOC105372861	XR_007068004.1	n.1293G>A		non_coding_transcript_exon_variant	1/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.658 AC: 100001 AN: 152034 Hom.: 33461 Cov.: 34

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.658 AC: 100108 AN: 152152 Hom.: 33512 Cov.: 34 AF XY: 0.660 AC XY: 49049 AN XY: 74370

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.785

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.636

Alfa AF: 0.609 Hom.: 28454

Bravo AF: 0.662

Asia WGS AF: 0.674 AC: 2344 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	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5748410; hg19: chr22-19718144;