rs9379002

Variant names:

• chr6-6012158-T-G
• rs9379002

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 0.369 in 151,966 control chromosomes in the GnomAD database, including 11,117 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 0.37 (11117 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 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: 0.369 AC: 56085 AN: 151848 Hom.: 11112 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.369 AC: 56122 AN: 151966 Hom.: 11117 Cov.: 32 AF XY: 0.367 AC XY: 27240 AN XY: 74274

African (AFR) AF: 0.508 AC: 21055 AN: 41432

American (AMR) AF: 0.336 AC: 5127 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1233 AN: 3468

East Asian (EAS) AF: 0.497 AC: 2566 AN: 5166

South Asian (SAS) AF: 0.375 AC: 1805 AN: 4808

European-Finnish (FIN) AF: 0.258 AC: 2719 AN: 10558

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20440 AN: 67946

Other (OTH) AF: 0.336 AC: 708 AN: 2106

Alfa AF: 0.325 Hom.: 31861

Bravo AF: 0.383

Asia WGS AF: 0.447 AC: 1556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.57
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs9379002; hg19: chr6-6012391;