7-86584299-T-C

Variant names:

• chr7-86584299-T-C
• rs6972995

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 0.278 in 152,044 control chromosomes in the GnomAD database, including 6,122 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 0.28 (6122 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405

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 (NFE) allele frequency at 95% confidence interval = 0.314 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: 0.278 AC: 42219 AN: 151926 Hom.: 6114 Cov.: 31

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.278 AC: 42251 AN: 152044 Hom.: 6122 Cov.: 31 AF XY: 0.275 AC XY: 20435 AN XY: 74306

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.264

Alfa AF: 0.290 Hom.: 3045

Bravo AF: 0.271

Asia WGS AF: 0.274 AC: 953 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	1.5
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6972995; hg19: chr7-86213615;