rs13247600

chr7-121310856-G-C

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 0.048 in 152,212 control chromosomes in the GnomAD database, including 239 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 0.048 (239 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0639 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: 0.0481 AC: 7312 AN: 152094 Hom.: 239 Cov.: 32

Gnomad AFR AF: 0.0119

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0363

Gnomad ASJ AF: 0.0662

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0369

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0655

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0480 AC: 7307 AN: 152212 Hom.: 239 Cov.: 32 AF XY: 0.0509 AC XY: 3784 AN XY: 74402

Gnomad4 AFR AF: 0.0119

Gnomad4 AMR AF: 0.0363

Gnomad4 ASJ AF: 0.0662

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0367

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.0655

Gnomad4 OTH AF: 0.0397

Alfa AF: 0.0505 Hom.: 28

Bravo AF: 0.0410

Asia WGS AF: 0.0140 AC: 50 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.7
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13247600; hg19: chr7-120950910;