rs9445708

Variant names:

• chr6-66415116-G-A
• rs9445708

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 0.119 in 151,804 control chromosomes in the GnomAD database, including 1,218 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 0.12 (1218 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 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: 0.119 AC: 18125 AN: 151686 Hom.: 1218 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0641

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0111

Gnomad SAS AF: 0.0423

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.119 AC: 18138 AN: 151804 Hom.: 1218 Cov.: 32 AF XY: 0.119 AC XY: 8809 AN XY: 74200

African (AFR) AF: 0.154 AC: 6370 AN: 41406

American (AMR) AF: 0.0639 AC: 973 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 390 AN: 3460

East Asian (EAS) AF: 0.0111 AC: 57 AN: 5126

South Asian (SAS) AF: 0.0427 AC: 206 AN: 4822

European-Finnish (FIN) AF: 0.148 AC: 1561 AN: 10578

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

European-Non Finnish (NFE) AF: 0.121 AC: 8240 AN: 67876

Other (OTH) AF: 0.108 AC: 228 AN: 2114

Alfa AF: 0.125 Hom.: 166

Bravo AF: 0.115

Asia WGS AF: 0.0420 AC: 145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.79
DANN	Benign	0.40
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs9445708; hg19: chr6-67125009;