rs10504216

Variant names:

• chr8-57068911-G-A
• rs10504216

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 0.0982 in 152,170 control chromosomes in the GnomAD database, including 886 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 0.098 (886 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 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: 0.0982 AC: 14930 AN: 152054 Hom.: 883 Cov.: 33

Gnomad AFR AF: 0.0299

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0711

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0982 AC: 14937 AN: 152170 Hom.: 886 Cov.: 33 AF XY: 0.101 AC XY: 7479 AN XY: 74406

Gnomad4 AFR AF: 0.0300

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.0710

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.106

Alfa AF: 0.124 Hom.: 1180

Bravo AF: 0.0915

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.6
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504216; hg19: chr8-57981470;