rs10504605

chr8-76019658-A-G

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 0.0545 in 152,158 control chromosomes in the GnomAD database, including 276 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 0.054 (276 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0545 AC: 8282 AN: 152040 Hom.: 275 Cov.: 32

Gnomad AFR AF: 0.0300

Gnomad AMI AF: 0.0485

Gnomad AMR AF: 0.0718

Gnomad ASJ AF: 0.0504

Gnomad EAS AF: 0.0445

Gnomad SAS AF: 0.0207

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0608

Gnomad OTH AF: 0.0646

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

GnomAD4 genome AF: 0.0545 AC: 8287 AN: 152158 Hom.: 276 Cov.: 32 AF XY: 0.0560 AC XY: 4168 AN XY: 74374

Gnomad4 AFR AF: 0.0299

Gnomad4 AMR AF: 0.0719

Gnomad4 ASJ AF: 0.0504

Gnomad4 EAS AF: 0.0446

Gnomad4 SAS AF: 0.0207

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0609

Gnomad4 OTH AF: 0.0639

Alfa AF: 0.0582 Hom.: 255

Bravo AF: 0.0546

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	17
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504605; hg19: chr8-76931893;