rs753733

chr19-7704680-G-A

Variant summary

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

The XR_936296.2(LOC105372262):n.738+112C>T 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 0.12 in 152,052 control chromosomes in the GnomAD database, including 1,304 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 0.12 (1304 hom., cov: 31)
• Consequence: LOC105372262 XR_936296.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.325

Genes affected

LOC105372262 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372262	XR_936296.2	n.738+112C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18201 AN: 151934 Hom.: 1301 Cov.: 31

Gnomad AFR AF: 0.0561

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.120 AC: 18202 AN: 152052 Hom.: 1304 Cov.: 31 AF XY: 0.121 AC XY: 8985 AN XY: 74314

Gnomad4 AFR AF: 0.0560

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.127

Alfa AF: 0.140 Hom.: 3177

Bravo AF: 0.110

Asia WGS AF: 0.165 AC: 573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.8
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs753733; hg19: chr19-7769566;