rs1633030

Variant names:

• chr6-29778017-T-C
• rs1633030

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 0.345 in 152,010 control chromosomes in the GnomAD database, including 9,527 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 0.35 (9527 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.457 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: 0.345 AC: 52444 AN: 151892 Hom.: 9519 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.345 AC: 52474 AN: 152010 Hom.: 9527 Cov.: 32 AF XY: 0.339 AC XY: 25180 AN XY: 74294

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.348

Alfa AF: 0.325 Hom.: 8170

Bravo AF: 0.361

Asia WGS AF: 0.257 AC: 896 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	0.40
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1633030; hg19: chr6-29745794;