chr7-86504710-G-A

Variant names:

• chr7-86504710-G-A
• rs10499898

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 0.0638 in 152,164 control chromosomes in the GnomAD database, including 403 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 0.064 (403 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0639 AC: 9716 AN: 152046 Hom.: 402 Cov.: 31

Gnomad AFR AF: 0.0210

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0344

Gnomad ASJ AF: 0.0568

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0217

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0983

Gnomad OTH AF: 0.0554

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

GnomAD4 genome AF: 0.0638 AC: 9715 AN: 152164 Hom.: 403 Cov.: 31 AF XY: 0.0623 AC XY: 4635 AN XY: 74406

Gnomad4 AFR AF: 0.0209

Gnomad4 AMR AF: 0.0343

Gnomad4 ASJ AF: 0.0568

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0220

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.0984

Gnomad4 OTH AF: 0.0548

Alfa AF: 0.0861 Hom.: 317

Bravo AF: 0.0571

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	-0.93
CADD	Benign	0.64
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499898; hg19: chr7-86134026;