rs9959776

Variant names:

• chr18-76001073-T-G
• rs9959776

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 0.383 in 152,026 control chromosomes in the GnomAD database, including 11,397 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 0.38 (11397 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 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: 0.383 AC: 58138 AN: 151908 Hom.: 11376 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.383 AC: 58190 AN: 152026 Hom.: 11397 Cov.: 32 AF XY: 0.377 AC XY: 28028 AN XY: 74332

African (AFR) AF: 0.420 AC: 17413 AN: 41442

American (AMR) AF: 0.369 AC: 5628 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1823 AN: 3464

East Asian (EAS) AF: 0.168 AC: 870 AN: 5180

South Asian (SAS) AF: 0.408 AC: 1966 AN: 4820

European-Finnish (FIN) AF: 0.271 AC: 2870 AN: 10574

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26408 AN: 67962

Other (OTH) AF: 0.389 AC: 820 AN: 2106

Alfa AF: 0.391 Hom.: 26035

Bravo AF: 0.393

Asia WGS AF: 0.285 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.14
DANN	Benign	0.56
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs9959776; hg19: chr18-73713028;