rs17236800

Positions:

• chr7-37904773-A-G

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 0.142 in 152,260 control chromosomes in the GnomAD database, including 1,735 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 0.14 (1735 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.887

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.182 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: 0.142 AC: 21643 AN: 152140 Hom.: 1733 Cov.: 32

Gnomad AFR AF: 0.0826

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.0804

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.142 AC: 21653 AN: 152260 Hom.: 1735 Cov.: 32 AF XY: 0.139 AC XY: 10334 AN XY: 74438

Gnomad4 AFR AF: 0.0825

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.0619

Gnomad4 SAS AF: 0.0804

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.147

Alfa AF: 0.173 Hom.: 3181

Bravo AF: 0.134

Asia WGS AF: 0.0740 AC: 260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.7
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17236800; hg19: chr7-37944375;