7-8988208-C-A

Variant names:

• chr7-8988208-C-A
• rs6979515

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 0.614 in 151,732 control chromosomes in the GnomAD database, including 28,686 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 0.61 (28686 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 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: 0.614 AC: 93099 AN: 151614 Hom.: 28649 Cov.: 30

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.614 AC: 93194 AN: 151732 Hom.: 28686 Cov.: 30 AF XY: 0.612 AC XY: 45345 AN XY: 74136

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.608

Alfa AF: 0.601 Hom.: 25381

Bravo AF: 0.611

Asia WGS AF: 0.631 AC: 2194 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6979515; hg19: chr7-9027838;