rs4802189

Variant names:

• chr19-43642778-C-A
• rs4802189
• ENST00000830541.1:n.91+2761C>A

Variant summary

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

The ENST00000830541.1(ENSG00000308028):​n.91+2761C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,138 control chromosomes in the GnomAD database, including 3,337 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 0.20 (3337 hom., cov: 32)
• Consequence: ENSG00000308028 ENST00000830541.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 14 publications found

Genes affected

ENSG00000308028 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) 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
ENSG00000308028	ENST00000830541.1	n.91+2761C>A		intron_variant	Intron 1 of 1
ENSG00000308028	ENST00000830542.1	n.50+2696C>A		intron_variant	Intron 1 of 1
ENSG00000308028	ENST00000830543.1	n.101+2454C>A		intron_variant	Intron 1 of 1
ENSG00000308028	ENST00000830544.1	n.56+2454C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30650 AN: 152020 Hom.: 3333 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0964

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.202 AC: 30674 AN: 152138 Hom.: 3337 Cov.: 32 AF XY: 0.200 AC XY: 14844 AN XY: 74370

African (AFR) AF: 0.269 AC: 11148 AN: 41492

American (AMR) AF: 0.252 AC: 3848 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 559 AN: 3466

East Asian (EAS) AF: 0.104 AC: 540 AN: 5180

South Asian (SAS) AF: 0.0968 AC: 467 AN: 4822

European-Finnish (FIN) AF: 0.137 AC: 1447 AN: 10584

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12013 AN: 68000

Other (OTH) AF: 0.217 AC: 458 AN: 2112

Alfa AF: 0.192 Hom.: 8585

Bravo AF: 0.219

Asia WGS AF: 0.133 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.9
DANN	Benign	0.55
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs4802189; hg19: chr19-44146930;