rs1535964

Variant names:

• chr9-114510159-G-C
• rs1535964

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 0.302 in 152,172 control chromosomes in the GnomAD database, including 7,593 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 0.30 (7593 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 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: 0.302 AC: 45968 AN: 152054 Hom.: 7595 Cov.: 33

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.0289

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.302 AC: 45952 AN: 152172 Hom.: 7593 Cov.: 33 AF XY: 0.302 AC XY: 22485 AN XY: 74406

African (AFR) AF: 0.199 AC: 8280 AN: 41534

American (AMR) AF: 0.302 AC: 4619 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1172 AN: 3466

East Asian (EAS) AF: 0.0286 AC: 148 AN: 5176

South Asian (SAS) AF: 0.213 AC: 1030 AN: 4826

European-Finnish (FIN) AF: 0.440 AC: 4654 AN: 10584

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 25017 AN: 67984

Other (OTH) AF: 0.301 AC: 636 AN: 2112

Alfa AF: 0.340 Hom.: 1157

Bravo AF: 0.285

Asia WGS AF: 0.139 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.8
DANN	Benign	0.57
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs1535964; hg19: chr9-117272439;