rs7003694

chr8-27489677-T-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 0.116 in 152,232 control chromosomes in the GnomAD database, including 1,071 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 0.12 (1071 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

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 (AFR) allele frequency at 95% confidence interval = 0.17 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: 0.116 AC: 17581 AN: 152114 Hom.: 1066 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0876

Gnomad ASJ AF: 0.0842

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.0851

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.116 AC: 17608 AN: 152232 Hom.: 1071 Cov.: 32 AF XY: 0.112 AC XY: 8373 AN XY: 74440

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.0875

Gnomad4 ASJ AF: 0.0842

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0638

Gnomad4 FIN AF: 0.0851

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.117

Alfa AF: 0.103 Hom.: 1523

Bravo AF: 0.118

Asia WGS AF: 0.0330 AC: 115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.76
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7003694; hg19: chr8-27347194;