rs13243044

Variant names:

• chr7-21045645-G-A
• rs13243044

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;