9-75661759-C-T

Variant names:

• chr9-75661759-C-T
• rs10512049

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 0.0593 in 152,184 control chromosomes in the GnomAD database, including 295 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 0.059 (295 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0686 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: 0.0593 AC: 9022 AN: 152066 Hom.: 295 Cov.: 32

Gnomad AFR AF: 0.0550

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0545

Gnomad ASJ AF: 0.0801

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0429

Gnomad FIN AF: 0.0334

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0703

Gnomad OTH AF: 0.0654

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

GnomAD4 genome AF: 0.0593 AC: 9026 AN: 152184 Hom.: 295 Cov.: 32 AF XY: 0.0576 AC XY: 4288 AN XY: 74414

Gnomad4 AFR AF: 0.0549

Gnomad4 AMR AF: 0.0544

Gnomad4 ASJ AF: 0.0801

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0434

Gnomad4 FIN AF: 0.0334

Gnomad4 NFE AF: 0.0703

Gnomad4 OTH AF: 0.0647

Alfa AF: 0.0659 Hom.: 570

Bravo AF: 0.0601

Asia WGS AF: 0.0240 AC: 84 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512049; hg19: chr9-78276675;