rs9384488

chr6-156688247-G-Achr6-156688247-G-Cchr6-156688247-G-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 0.48 in 152,102 control chromosomes in the GnomAD database, including 20,525 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 0.48 (20525 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72

ACMG classification

Verdict is Benign. Variant got -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 = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72827 AN: 151982 Hom.: 20476 Cov.: 32

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.480 AC: 72933 AN: 152102 Hom.: 20525 Cov.: 32 AF XY: 0.477 AC XY: 35439 AN XY: 74368

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.435

Alfa AF: 0.373 Hom.: 14826

Bravo AF: 0.493

Asia WGS AF: 0.599 AC: 2079 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	0.029
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9384488; hg19: chr6-157009381;