rs7498886

chr16-62045298-A-Gchr16-62045298-A-T

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 0.56 in 151,694 control chromosomes in the GnomAD database, including 26,542 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 0.56 (26542 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

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: 0.560 AC: 84860 AN: 151576 Hom.: 26491 Cov.: 30

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.603

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.560 AC: 84964 AN: 151694 Hom.: 26542 Cov.: 30 AF XY: 0.554 AC XY: 41062 AN XY: 74080

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.528

Alfa AF: 0.470 Hom.: 9110

Bravo AF: 0.575

Asia WGS AF: 0.434 AC: 1512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.046
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7498886; hg19: chr16-62079202;