rs10512077

Positions:

• chr9-78936744-G-A
• chr9-78936744-G-T

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 0.471 in 151,746 control chromosomes in the GnomAD database, including 18,229 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 0.47 (18229 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261

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 = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71377 AN: 151628 Hom.: 18191 Cov.: 31

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.471 AC: 71468 AN: 151746 Hom.: 18229 Cov.: 31 AF XY: 0.465 AC XY: 34480 AN XY: 74160

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.446

Alfa AF: 0.229 Hom.: 438

Bravo AF: 0.481

Asia WGS AF: 0.370 AC: 1290 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	1.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512077; hg19: chr9-81551660;