rs17869724

chr7-127284650-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0209 in 152,168 control chromosomes in the GnomAD database, including 52 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 0.021 (52 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.767

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0209 (3186/152168) while in subpopulation AFR AF= 0.039 (1621/41512). AF 95% confidence interval is 0.0375. There are 52 homozygotes in gnomad4. There are 1572 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 51 gene

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: 0.0208 AC: 3168 AN: 152050 Hom.: 51 Cov.: 32

Gnomad AFR AF: 0.0388

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.0233

Gnomad ASJ AF: 0.00836

Gnomad EAS AF: 0.0260

Gnomad SAS AF: 0.00977

Gnomad FIN AF: 0.0139

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0113

Gnomad OTH AF: 0.0186

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

GnomAD4 genome AF: 0.0209 AC: 3186 AN: 152168 Hom.: 52 Cov.: 32 AF XY: 0.0211 AC XY: 1572 AN XY: 74394

Gnomad4 AFR AF: 0.0390

Gnomad4 AMR AF: 0.0233

Gnomad4 ASJ AF: 0.00836

Gnomad4 EAS AF: 0.0259

Gnomad4 SAS AF: 0.0102

Gnomad4 FIN AF: 0.0139

Gnomad4 NFE AF: 0.0113

Gnomad4 OTH AF: 0.0194

Alfa AF: 0.0191 Hom.: 5

Bravo AF: 0.0227

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.16
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17869724; hg19: chr7-126924704;