rs6830890

Variant names:

• chr4-111597970-G-A
• rs6830890
• ENST00000681880.1:n.171-20535G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000681880.1(ENSG00000248656):​n.171-20535G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 151,728 control chromosomes in the GnomAD database, including 1,275 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 0.12 (1275 hom., cov: 31)
• Consequence: ENSG00000248656 ENST00000681880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

Genes affected

ENSG00000248656 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 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
ENSG00000248656	ENST00000681880.1	n.171-20535G>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17767 AN: 151610 Hom.: 1268 Cov.: 31

Gnomad AFR AF: 0.0442

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.0761

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.117 AC: 17786 AN: 151728 Hom.: 1275 Cov.: 31 AF XY: 0.124 AC XY: 9212 AN XY: 74104

Gnomad4 AFR AF: 0.0442

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.0761

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.0997

Alfa AF: 0.122 Hom.: 1479

Bravo AF: 0.110

Asia WGS AF: 0.164 AC: 569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6830890; hg19: chr4-112519126;