rs7185124

Positions:

• chr16-13656837-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 0.781 in 152,178 control chromosomes in the GnomAD database, including 46,540 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 0.78 (46540 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 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: 0.781 AC: 118808 AN: 152060 Hom.: 46493 Cov.: 33

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.781 AC: 118912 AN: 152178 Hom.: 46540 Cov.: 33 AF XY: 0.784 AC XY: 58353 AN XY: 74406

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.800

Gnomad4 ASJ AF: 0.756

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.765

Gnomad4 NFE AF: 0.761

Gnomad4 OTH AF: 0.762

Alfa AF: 0.772 Hom.: 22576

Bravo AF: 0.787

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.97
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7185124; hg19: chr16-13750694;