rs416115

Variant names:

• chr6-89175518-T-C
• rs416115

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.334 in 152,022 control chromosomes in the GnomAD database, including 8,852 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 0.33 (8852 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309
• 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).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

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: 0.334 AC: 50782 AN: 151904 Hom.: 8855 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.334 AC: 50803 AN: 152022 Hom.: 8852 Cov.: 32 AF XY: 0.346 AC XY: 25676 AN XY: 74292

African (AFR) AF: 0.328 AC: 13595 AN: 41458

American (AMR) AF: 0.352 AC: 5371 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 896 AN: 3466

East Asian (EAS) AF: 0.629 AC: 3262 AN: 5184

South Asian (SAS) AF: 0.362 AC: 1743 AN: 4812

European-Finnish (FIN) AF: 0.445 AC: 4693 AN: 10546

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20198 AN: 67970

Other (OTH) AF: 0.304 AC: 642 AN: 2110

Alfa AF: 0.308 Hom.: 28085

Bravo AF: 0.327

Asia WGS AF: 0.432 AC: 1504 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	0.84
DANN	Benign	0.52
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs416115; hg19: chr6-89885237;