chr7-86543860-C-T

Position:

• chr7-86543860-C-T

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 0.0625 in 152,240 control chromosomes in the GnomAD database, including 395 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 0.062 (395 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.86543860C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0625 AC: 9514 AN: 152122 Hom.: 394 Cov.: 32

Gnomad AFR AF: 0.0165

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0335

Gnomad ASJ AF: 0.0567

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0216

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0984

Gnomad OTH AF: 0.0540

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

GnomAD4 genome AF: 0.0625 AC: 9513 AN: 152240 Hom.: 395 Cov.: 32 AF XY: 0.0609 AC XY: 4530 AN XY: 74408

Gnomad4 AFR AF: 0.0164

Gnomad4 AMR AF: 0.0334

Gnomad4 ASJ AF: 0.0567

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0218

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.0984

Gnomad4 OTH AF: 0.0534

Alfa AF: 0.0776 Hom.: 293

Bravo AF: 0.0557

Asia WGS AF: 0.0120 AC: 42 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	13
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1527769; hg19: chr7-86173176;