chr6-30089898-C-T

Position:

• chr6-30089898-C-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 0.052 in 152,208 control chromosomes in the GnomAD database, including 252 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 0.052 (252 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0643 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: 0.0519 AC: 7898 AN: 152090 Hom.: 251 Cov.: 32

Gnomad AFR AF: 0.0494

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0675

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0364

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0238

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0516

Gnomad OTH AF: 0.0598

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

GnomAD4 genome AF: 0.0520 AC: 7912 AN: 152208 Hom.: 252 Cov.: 32 AF XY: 0.0518 AC XY: 3855 AN XY: 74406

Gnomad4 AFR AF: 0.0494

Gnomad4 AMR AF: 0.0678

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.0365

Gnomad4 SAS AF: 0.0239

Gnomad4 FIN AF: 0.0238

Gnomad4 NFE AF: 0.0516

Gnomad4 OTH AF: 0.0587

Alfa AF: 0.0572 Hom.: 85

Bravo AF: 0.0545

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.8
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9261365; hg19: chr6-30057675;