rs72699186

Variant names:

• chr9-6175855-A-T
• rs72699186

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 0.145 in 152,122 control chromosomes in the GnomAD database, including 1,744 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 0.15 (1744 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457
• Publications: 19 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 = 0.156 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: 0.145 AC: 22050 AN: 152004 Hom.: 1745 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.145 AC: 22062 AN: 152122 Hom.: 1744 Cov.: 31 AF XY: 0.146 AC XY: 10868 AN XY: 74390

African (AFR) AF: 0.132 AC: 5491 AN: 41538

American (AMR) AF: 0.136 AC: 2073 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3472

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5186

South Asian (SAS) AF: 0.148 AC: 713 AN: 4824

European-Finnish (FIN) AF: 0.165 AC: 1736 AN: 10522

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.159 AC: 10804 AN: 67978

Other (OTH) AF: 0.148 AC: 311 AN: 2108

Alfa AF: 0.146 Hom.: 196

Bravo AF: 0.143

Asia WGS AF: 0.0630 AC: 221 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.3
DANN	Benign	0.66
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs72699186; hg19: chr9-6175855;