rs1748722

Variant names:

• chr13-70998252-G-A
• rs1748722

Your query was ambiguous. Multiple possible variants found:

• chr13-70998252-G-A
• chr13-70998252-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0932 AC: 3867 AN: 41490

American (AMR) AF: 0.128 AC: 1960 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3470

East Asian (EAS) AF: 0.120 AC: 617 AN: 5162

South Asian (SAS) AF: 0.180 AC: 870 AN: 4824

European-Finnish (FIN) AF: 0.125 AC: 1330 AN: 10600

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11966 AN: 67972

Other (OTH) AF: 0.157 AC: 332 AN: 2110

Alfa AF: 0.0755 Hom.: 94

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
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs1748722; hg19: chr13-71572384;