rs6974002

Variant names:

• chr7-20326905-A-G
• rs6974002

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;