rs2619367

Variant names:

• chr4-89845944-A-C
• rs2619367
• ENST00000776860.1:n.209-4982T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-89845944-A-C
• chr4-89845944-A-G

Variant summary

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

The ENST00000776860.1(ENSG00000301182):​n.209-4982T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 151,848 control chromosomes in the GnomAD database, including 3,327 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 0.19 (3327 hom., cov: 30)
• Consequence: ENSG00000301182 ENST00000776860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 7 publications found

Genes affected

ENSG00000301182 (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 (NFE) allele frequency at 95% confidence interval = 0.265 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
ENSG00000301182	ENST00000776860.1	n.209-4982T>G		intron_variant	Intron 1 of 1
ENSG00000301182	ENST00000776861.1	n.183-4982T>G		intron_variant	Intron 1 of 1
ENSG00000301182	ENST00000776862.1	n.204-4982T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28275 AN: 151732 Hom.: 3325 Cov.: 30

Gnomad AFR AF: 0.0659

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.186 AC: 28290 AN: 151848 Hom.: 3327 Cov.: 30 AF XY: 0.184 AC XY: 13650 AN XY: 74212

African (AFR) AF: 0.0658 AC: 2727 AN: 41428

American (AMR) AF: 0.176 AC: 2675 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 713 AN: 3470

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5172

South Asian (SAS) AF: 0.123 AC: 592 AN: 4810

European-Finnish (FIN) AF: 0.243 AC: 2556 AN: 10526

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18216 AN: 67914

Other (OTH) AF: 0.205 AC: 433 AN: 2110

Alfa AF: 0.116 Hom.: 249

Bravo AF: 0.179

Asia WGS AF: 0.0610 AC: 214 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.68
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2619367; hg19: chr4-90767095;