rs570677

Variant names:

• chr10-78862599-C-T
• rs570677

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 0.427 in 152,174 control chromosomes in the GnomAD database, including 18,208 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 0.43 (18208 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422

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 (AFR) allele frequency at 95% confidence interval = 0.775 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: 0.426 AC: 64846 AN: 152056 Hom.: 18148 Cov.: 33

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.427 AC: 64968 AN: 152174 Hom.: 18208 Cov.: 33 AF XY: 0.429 AC XY: 31900 AN XY: 74388

Gnomad4 AFR AF: 0.782

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.647

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.374

Alfa AF: 0.290 Hom.: 8616

Bravo AF: 0.443

Asia WGS AF: 0.595 AC: 2066 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	1.8
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs570677; hg19: chr10-80622356;