chr10-87555668-G-T

Variant names:

• chr10-87555668-G-T
• rs2077871

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 0.603 in 151,590 control chromosomes in the GnomAD database, including 27,815 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 0.60 (27815 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.477

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.691 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: 0.603 AC: 91285 AN: 151472 Hom.: 27782 Cov.: 30

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.603 AC: 91372 AN: 151590 Hom.: 27815 Cov.: 30 AF XY: 0.603 AC XY: 44636 AN XY: 74034

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.554

Gnomad4 OTH AF: 0.582

Alfa AF: 0.554 Hom.: 20619

Bravo AF: 0.613

Asia WGS AF: 0.597 AC: 2072 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2077871; hg19: chr10-89315425;