rs236572

Variant names:

• chr17-70228951-C-T
• rs236572

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 0.412 in 151,984 control chromosomes in the GnomAD database, including 12,928 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 0.41 (12928 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 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: 0.412 AC: 62533 AN: 151866 Hom.: 12907 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.412 AC: 62597 AN: 151984 Hom.: 12928 Cov.: 32 AF XY: 0.414 AC XY: 30722 AN XY: 74270

African (AFR) AF: 0.381 AC: 15782 AN: 41442

American (AMR) AF: 0.413 AC: 6304 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1540 AN: 3472

East Asian (EAS) AF: 0.257 AC: 1328 AN: 5160

South Asian (SAS) AF: 0.382 AC: 1841 AN: 4820

European-Finnish (FIN) AF: 0.505 AC: 5334 AN: 10556

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29138 AN: 67948

Other (OTH) AF: 0.392 AC: 828 AN: 2114

Alfa AF: 0.422 Hom.: 2139

Bravo AF: 0.404

Asia WGS AF: 0.333 AC: 1154 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.5
DANN	Benign	0.63
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs236572; hg19: chr17-68225092;