rs13243044

chr7-21045645-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.204 in 152,154 control chromosomes in the GnomAD database, including 3,267 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 0.20 (3267 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.32

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 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: 0.204 AC: 30979 AN: 152036 Hom.: 3260 Cov.: 33

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.204 AC: 31013 AN: 152154 Hom.: 3267 Cov.: 33 AF XY: 0.205 AC XY: 15244 AN XY: 74388

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.179

Alfa AF: 0.184 Hom.: 3476

Bravo AF: 0.195

Asia WGS AF: 0.191 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
Cadd	Benign	19
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13243044; hg19: chr7-21085264;