rs1233708

chr6-28205441-G-A

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 0.339 in 152,008 control chromosomes in the GnomAD database, including 9,562 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 0.34 (9562 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 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: 0.339 AC: 51466 AN: 151890 Hom.: 9526 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.339 AC: 51560 AN: 152008 Hom.: 9562 Cov.: 32 AF XY: 0.335 AC XY: 24886 AN XY: 74302

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.319

Alfa AF: 0.278 Hom.: 8463

Bravo AF: 0.353

Asia WGS AF: 0.326 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.62
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: rs1233708; hg19: chr6-28173219;