chr6-29816415-C-G

Variant names:

• chr6-29816415-C-G
• rs1633097

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 0.493 in 151,682 control chromosomes in the GnomAD database, including 18,762 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 0.49 (18762 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.684

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.595 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: 0.493 AC: 74694 AN: 151566 Hom.: 18733 Cov.: 33

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.493 AC: 74768 AN: 151682 Hom.: 18762 Cov.: 33 AF XY: 0.488 AC XY: 36194 AN XY: 74108

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.521

Alfa AF: 0.245 Hom.: 398

Bravo AF: 0.515

Asia WGS AF: 0.566 AC: 1971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1633097; hg19: chr6-29784192;