9-75661759-C-T

Variant names:

• chr9-75661759-C-T
• rs10512049

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0549 AC: 2281 AN: 41532

American (AMR) AF: 0.0544 AC: 831 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0801 AC: 278 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.0434 AC: 209 AN: 4820

European-Finnish (FIN) AF: 0.0334 AC: 354 AN: 10596

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0703 AC: 4780 AN: 67982

Other (OTH) AF: 0.0647 AC: 137 AN: 2116

Alfa AF: 0.0653 Hom.: 870

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
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10512049; hg19: chr9-78276675;