rs1748722

chr13-70998252-G-Achr13-70998252-G-T

Variant summary

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

The variant allele was found at a frequency of 0.143 in 152,102 control chromosomes in the GnomAD database, including 1,663 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 0.14 (1663 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614

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 (SAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21731 AN: 151984 Hom.: 1660 Cov.: 32

Gnomad AFR AF: 0.0930

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.143 AC: 21755 AN: 152102 Hom.: 1663 Cov.: 32 AF XY: 0.141 AC XY: 10489 AN XY: 74350

Gnomad4 AFR AF: 0.0932

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.157

Alfa AF: 0.0748 Hom.: 91

Bravo AF: 0.141

Asia WGS AF: 0.143 AC: 495 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	1.8
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1748722; hg19: chr13-71572384;