6-30971106-A-G

Position:

• chr6-30971106-A-G

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 0.107 in 152,252 control chromosomes in the GnomAD database, including 1,218 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 0.11 (1218 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.318 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: 0.107 AC: 16266 AN: 152134 Hom.: 1220 Cov.: 32

Gnomad AFR AF: 0.0290

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.0802

Gnomad ASJ AF: 0.0952

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.0943

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

GnomAD4 genome AF: 0.107 AC: 16256 AN: 152252 Hom.: 1218 Cov.: 32 AF XY: 0.111 AC XY: 8240 AN XY: 74434

Gnomad4 AFR AF: 0.0289

Gnomad4 AMR AF: 0.0799

Gnomad4 ASJ AF: 0.0952

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.0961

Alfa AF: 0.124 Hom.: 1586

Bravo AF: 0.0965

Asia WGS AF: 0.214 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.3
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9368649; hg19: chr6-30938883;