rs7005198

chr8-16988800-G-Cchr8-16988800-G-T

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 0.202 in 152,070 control chromosomes in the GnomAD database, including 3,526 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 (3526 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 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: 0.202 AC: 30728 AN: 151952 Hom.: 3521 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.202 AC: 30748 AN: 152070 Hom.: 3526 Cov.: 32 AF XY: 0.211 AC XY: 15683 AN XY: 74312

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.208

Alfa AF: 0.130 Hom.: 238

Bravo AF: 0.190

Asia WGS AF: 0.352 AC: 1223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.8
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7005198; hg19: chr8-16846309;