rs1816678

Variant names:

• chr5-111060457-A-G
• rs1816678

Your query was ambiguous. Multiple possible variants found:

• chr5-111060457-A-G
• chr5-111060457-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 0.619 in 152,138 control chromosomes in the GnomAD database, including 30,687 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 0.62 (30687 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 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: 0.619 AC: 94102 AN: 152020 Hom.: 30652 Cov.: 33

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.619 AC: 94186 AN: 152138 Hom.: 30687 Cov.: 33 AF XY: 0.618 AC XY: 45937 AN XY: 74372

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.610

Alfa AF: 0.567 Hom.: 3150

Bravo AF: 0.644

Asia WGS AF: 0.580 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0030
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1816678; hg19: chr5-110396155;