rs9379053

Variant names:

• chr6-6663797-T-C
• rs9379053

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 0.122 in 152,152 control chromosomes in the GnomAD database, including 1,258 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 (1258 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.212 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: 0.122 AC: 18571 AN: 152034 Hom.: 1255 Cov.: 31

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.0925

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.122 AC: 18584 AN: 152152 Hom.: 1258 Cov.: 31 AF XY: 0.124 AC XY: 9257 AN XY: 74382

African (AFR) AF: 0.105 AC: 4363 AN: 41490

American (AMR) AF: 0.164 AC: 2501 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 405 AN: 3472

East Asian (EAS) AF: 0.183 AC: 944 AN: 5168

South Asian (SAS) AF: 0.223 AC: 1073 AN: 4818

European-Finnish (FIN) AF: 0.0925 AC: 980 AN: 10590

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7860 AN: 68006

Other (OTH) AF: 0.116 AC: 246 AN: 2112

Alfa AF: 0.121 Hom.: 2300

Bravo AF: 0.126

Asia WGS AF: 0.180 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.3
DANN	Benign	0.68
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs9379053; hg19: chr6-6664030;