rs6974002

Positions:

• chr7-20326905-A-G

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 0.252 in 152,100 control chromosomes in the GnomAD database, including 5,186 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 0.25 (5186 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38296 AN: 151982 Hom.: 5178 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.252 AC: 38335 AN: 152100 Hom.: 5186 Cov.: 32 AF XY: 0.254 AC XY: 18912 AN XY: 74362

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.249

Alfa AF: 0.213 Hom.: 5043

Bravo AF: 0.261

Asia WGS AF: 0.255 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6974002; hg19: chr7-20366528;