rs75598935

Positions:

• chr15-79927251-G-A

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 0.0218 in 152,276 control chromosomes in the GnomAD database, including 78 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 0.022 (78 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0218 (3317/152276) while in subpopulation SAS AF= 0.0323 (156/4832). AF 95% confidence interval is 0.0282. There are 78 homozygotes in gnomad4. There are 1868 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 78 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: 0.0218 AC: 3317 AN: 152158 Hom.: 78 Cov.: 31

Gnomad AFR AF: 0.00396

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0107

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0323

Gnomad FIN AF: 0.0985

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0255

Gnomad OTH AF: 0.0153

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

GnomAD4 genome AF: 0.0218 AC: 3317 AN: 152276 Hom.: 78 Cov.: 31 AF XY: 0.0251 AC XY: 1868 AN XY: 74450

Gnomad4 AFR AF: 0.00395

Gnomad4 AMR AF: 0.0107

Gnomad4 ASJ AF: 0.00576

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0323

Gnomad4 FIN AF: 0.0985

Gnomad4 NFE AF: 0.0255

Gnomad4 OTH AF: 0.0151

Alfa AF: 0.0257 Hom.: 12

Bravo AF: 0.0134

Asia WGS AF: 0.00953 AC: 33 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.33
DANN	Benign	0.97

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs75598935; hg19: chr15-80219593;