rs9986182

Variant names:

• chr5-35245578-G-A
• rs9986182

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 0.278 in 152,022 control chromosomes in the GnomAD database, including 6,746 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 0.28 (6746 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.46 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: 0.278 AC: 42246 AN: 151904 Hom.: 6745 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.0863

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.278 AC: 42249 AN: 152022 Hom.: 6746 Cov.: 32 AF XY: 0.277 AC XY: 20612 AN XY: 74304

African (AFR) AF: 0.145 AC: 5996 AN: 41472

American (AMR) AF: 0.256 AC: 3916 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1276 AN: 3466

East Asian (EAS) AF: 0.0861 AC: 445 AN: 5166

South Asian (SAS) AF: 0.476 AC: 2289 AN: 4808

European-Finnish (FIN) AF: 0.276 AC: 2909 AN: 10546

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24361 AN: 67974

Other (OTH) AF: 0.308 AC: 651 AN: 2114

Alfa AF: 0.302 Hom.: 905

Bravo AF: 0.264

Asia WGS AF: 0.288 AC: 999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8
DANN	Benign	0.50
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs9986182; hg19: chr5-35245680; COSMIC: COSV53477647;