rs35915

Positions:

• chr16-55639423-T-A
• chr16-55639423-T-C

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 0.116 in 152,100 control chromosomes in the GnomAD database, including 1,242 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 0.12 (1242 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185

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 = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17604 AN: 151982 Hom.: 1241 Cov.: 31

Gnomad AFR AF: 0.0395

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.116 AC: 17609 AN: 152100 Hom.: 1242 Cov.: 31 AF XY: 0.114 AC XY: 8440 AN XY: 74340

Gnomad4 AFR AF: 0.0394

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0658 Hom.: 77

Bravo AF: 0.111

Asia WGS AF: 0.130 AC: 452 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	3.0
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35915; hg19: chr16-55673335;