rs72699186

Positions:

• chr9-6175855-A-T

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.6175855A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.148

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72699186; hg19: chr9-6175855;