rs767770

Variant names:

• chr9-121336257-C-T
• rs767770

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 0.0962 in 152,112 control chromosomes in the GnomAD database, including 1,084 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 0.096 (1084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 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: 0.0961 AC: 14605 AN: 151994 Hom.: 1081 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0643

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.0724

Gnomad FIN AF: 0.0517

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0429

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0962 AC: 14633 AN: 152112 Hom.: 1084 Cov.: 32 AF XY: 0.0956 AC XY: 7111 AN XY: 74362

African (AFR) AF: 0.200 AC: 8304 AN: 41438

American (AMR) AF: 0.0642 AC: 981 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 462 AN: 3472

East Asian (EAS) AF: 0.159 AC: 825 AN: 5178

South Asian (SAS) AF: 0.0717 AC: 346 AN: 4828

European-Finnish (FIN) AF: 0.0517 AC: 547 AN: 10586

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0429 AC: 2918 AN: 67998

Other (OTH) AF: 0.102 AC: 215 AN: 2114

Alfa AF: 0.0674 Hom.: 1063

Bravo AF: 0.101

Asia WGS AF: 0.107 AC: 371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.52
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs767770; hg19: chr9-124098535;