rs10499898

Variant names:

• chr7-86504710-G-A
• rs10499898

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 0.0638 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0209 AC: 869 AN: 41530

American (AMR) AF: 0.0343 AC: 524 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0568 AC: 197 AN: 3470

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5176

South Asian (SAS) AF: 0.0220 AC: 106 AN: 4828

European-Finnish (FIN) AF: 0.105 AC: 1110 AN: 10568

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0984 AC: 6687 AN: 67988

Other (OTH) AF: 0.0548 AC: 116 AN: 2116

Alfa AF: 0.0858 Hom.: 348

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
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs10499898; hg19: chr7-86134026;