rs17869724

Variant names:

• chr7-127284650-C-T
• rs17869724

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 52 gene

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: 0.0208 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

African (AFR) AF: 0.0390 AC: 1621 AN: 41512

American (AMR) AF: 0.0233 AC: 356 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.00836 AC: 29 AN: 3470

East Asian (EAS) AF: 0.0259 AC: 134 AN: 5172

South Asian (SAS) AF: 0.0102 AC: 49 AN: 4806

European-Finnish (FIN) AF: 0.0139 AC: 147 AN: 10600

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0113 AC: 769 AN: 68016

Other (OTH) AF: 0.0194 AC: 41 AN: 2114

Alfa AF: 0.0181 Hom.: 10

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
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs17869724; hg19: chr7-126924704;