rs7648568

chr3-137341847-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.184 in 152,122 control chromosomes in the GnomAD database, including 2,808 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 0.18 (2808 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.15

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.17).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.378 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: 0.185 AC: 28053 AN: 152004 Hom.: 2803 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.184 AC: 28063 AN: 152122 Hom.: 2808 Cov.: 33 AF XY: 0.187 AC XY: 13897 AN XY: 74384

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.183

Alfa AF: 0.0940 Hom.: 131

Bravo AF: 0.183

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.17
Cadd	Uncertain	24
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7648568; hg19: chr3-137060689;