rs6820379

Variant names:

• chr4-105120082-A-G
• rs6820379
• ENST00000506148.6:n.*78A>G

Variant summary

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

The ENST00000506386.1(ENSG00000248373):​n.*82A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,210 control chromosomes in the GnomAD database, including 1,459 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 0.10 (1459 hom., cov: 33)
  • Exomes 𝑓: 0.083 (0 hom.)
• Consequence: ENSG00000248373 ENST00000506386.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 0 publications found

Genes affected

ENSG00000248373 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000506386.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248373	ENST00000506148.6	TSL:5	n.*78A>G		downstream_gene	N/A
	ENSG00000248373	ENST00000506386.1	TSL:3	n.*82A>G		downstream_gene	N/A
	ENSG00000248373	ENST00000671069.2		n.*78A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15236 AN: 152080 Hom.: 1455 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0452

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0377

Gnomad FIN AF: 0.0436

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0384

Gnomad OTH AF: 0.0783

GnomAD4 exome AF: 0.0833 AC: 1 AN: 12 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0833 AC: 1 AN: 12

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.100 AC: 15256 AN: 152198 Hom.: 1459 Cov.: 33 AF XY: 0.0989 AC XY: 7358 AN XY: 74428

African (AFR) AF: 0.257 AC: 10661 AN: 41498

American (AMR) AF: 0.0452 AC: 691 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 377 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.0377 AC: 182 AN: 4822

European-Finnish (FIN) AF: 0.0436 AC: 463 AN: 10610

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0384 AC: 2609 AN: 67998

Other (OTH) AF: 0.0775 AC: 164 AN: 2116

Alfa AF: 0.0579 Hom.: 281

Bravo AF: 0.108

Asia WGS AF: 0.0270 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.24
DANN	Benign	0.56
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6820379;

hg19: chr4-106041239;