rs9389835

chr6-140949523-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.369 in 152,024 control chromosomes in the GnomAD database, including 10,784 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 (10784 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.96

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 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: 0.370 AC: 56143 AN: 151906 Hom.: 10786 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.369 AC: 56167 AN: 152024 Hom.: 10784 Cov.: 32 AF XY: 0.361 AC XY: 26825 AN XY: 74302

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.365

Alfa AF: 0.367 Hom.: 20986

Bravo AF: 0.370

Asia WGS AF: 0.266 AC: 925 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
Cadd	Benign	17
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9389835; hg19: chr6-141270660;