rs1233708

Variant names:

• chr6-28205441-G-A
• rs1233708

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 28 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.496 AC: 20539 AN: 41444

American (AMR) AF: 0.327 AC: 4996 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 760 AN: 3470

East Asian (EAS) AF: 0.299 AC: 1547 AN: 5172

South Asian (SAS) AF: 0.281 AC: 1354 AN: 4822

European-Finnish (FIN) AF: 0.270 AC: 2848 AN: 10554

Middle Eastern (MID) AF: 0.202 AC: 59 AN: 292

European-Non Finnish (NFE) AF: 0.271 AC: 18442 AN: 67950

Other (OTH) AF: 0.319 AC: 671 AN: 2104

Alfa AF: 0.300 Hom.: 15726

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1233708; hg19: chr6-28173219;