rs6862199

Variant names:

• chr5-56713185-T-C
• rs6862199
• ENST00000821819.1:n.61+12778A>G

Variant summary

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

The ENST00000821819.1(ENSG00000306891):​n.61+12778A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,966 control chromosomes in the GnomAD database, including 18,254 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 0.48 (18254 hom., cov: 31)
• Consequence: ENSG00000306891 ENST00000821819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• Publications: 9 publications found

Genes affected

ENSG00000306891 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821819.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306891	ENST00000821819.1		n.61+12778A>G		intron	N/A
	ENSG00000306891	ENST00000821820.1		n.93+12778A>G		intron	N/A
	ENSG00000306891	ENST00000821821.1		n.143+12778A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72378 AN: 151848 Hom.: 18244 Cov.: 31

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.476 AC: 72408 AN: 151966 Hom.: 18254 Cov.: 31 AF XY: 0.470 AC XY: 34939 AN XY: 74280

African (AFR) AF: 0.339 AC: 14062 AN: 41464

American (AMR) AF: 0.523 AC: 7993 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1979 AN: 3464

East Asian (EAS) AF: 0.195 AC: 1007 AN: 5152

South Asian (SAS) AF: 0.421 AC: 2026 AN: 4814

European-Finnish (FIN) AF: 0.487 AC: 5148 AN: 10560

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38534 AN: 67930

Other (OTH) AF: 0.501 AC: 1059 AN: 2114

Alfa AF: 0.539 Hom.: 75318

Bravo AF: 0.474

Asia WGS AF: 0.324 AC: 1125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.62
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs6862199; hg19: chr5-56009012;