rs9381981

chr6-51519369-T-Achr6-51519369-T-C

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 0.378 in 151,968 control chromosomes in the GnomAD database, including 10,896 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 0.38 (10896 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 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: 0.378 AC: 57342 AN: 151850 Hom.: 10892 Cov.: 31

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.378 AC: 57372 AN: 151968 Hom.: 10896 Cov.: 31 AF XY: 0.372 AC XY: 27649 AN XY: 74288

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.376

Alfa AF: 0.261 Hom.: 612

Bravo AF: 0.376

Asia WGS AF: 0.337 AC: 1171 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.6
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9381981; hg19: chr6-51384167;