rs6974002

Variant names:

• chr7-20326905-A-G
• rs6974002

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.329 AC: 13648 AN: 41452

American (AMR) AF: 0.279 AC: 4258 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 973 AN: 3468

East Asian (EAS) AF: 0.370 AC: 1912 AN: 5166

South Asian (SAS) AF: 0.216 AC: 1043 AN: 4824

European-Finnish (FIN) AF: 0.218 AC: 2307 AN: 10590

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.195 AC: 13249 AN: 68004

Other (OTH) AF: 0.249 AC: 525 AN: 2112

Alfa AF: 0.220 Hom.: 7378

Bravo AF: 0.261

Asia WGS AF: 0.255 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.75
PhyloP100		-0.023

Splicing

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

Other links and lift over

dbSNP: rs6974002; hg19: chr7-20366528;