rs9397674

Variant names:

• chr6-153945865-C-T
• rs9397674

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 0.236 in 152,056 control chromosomes in the GnomAD database, including 4,546 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 0.24 (4546 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.39 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: 0.236 AC: 35812 AN: 151938 Hom.: 4535 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.236 AC: 35828 AN: 152056 Hom.: 4546 Cov.: 32 AF XY: 0.244 AC XY: 18165 AN XY: 74334

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.267

Alfa AF: 0.215 Hom.: 543

Bravo AF: 0.239

Asia WGS AF: 0.377 AC: 1311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9397674; hg19: chr6-154267000;