chr6-30411297-T-C

Position:

• chr6-30411297-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 0.161 in 152,108 control chromosomes in the GnomAD database, including 2,121 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 0.16 (2121 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24404 AN: 151990 Hom.: 2119 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0312

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0891

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.161 AC: 24419 AN: 152108 Hom.: 2121 Cov.: 32 AF XY: 0.156 AC XY: 11608 AN XY: 74368

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.0315

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.0891

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.152

Alfa AF: 0.154 Hom.: 1085

Bravo AF: 0.168

Asia WGS AF: 0.0730 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9261821; hg19: chr6-30379074;