rs753733

Variant names:

• chr19-7704680-G-A
• rs753733
• XR_936296.2:n.738+112C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_936296.2(LOC105372262):​n.738+112C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.325
• Publications: 7 publications found

Genes affected

LOC105372262 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105372262	XR_936296.2	n.738+112C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0560 AC: 2324 AN: 41494

American (AMR) AF: 0.105 AC: 1603 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3466

East Asian (EAS) AF: 0.116 AC: 599 AN: 5156

South Asian (SAS) AF: 0.244 AC: 1175 AN: 4808

European-Finnish (FIN) AF: 0.150 AC: 1588 AN: 10578

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9929 AN: 67958

Other (OTH) AF: 0.127 AC: 268 AN: 2110

Alfa AF: 0.135 Hom.: 4742

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
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs753733; hg19: chr19-7769566;