rs4384980

Variant names:

• chr3-182741281-A-C
• rs4384980
• ENST00000788512.1:n.206+37576A>C

Your query was ambiguous. Multiple possible variants found:

• chr3-182741281-A-C
• chr3-182741281-A-T

Variant summary

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

The ENST00000788512.1(ENSG00000302649):​n.206+37576A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,480 control chromosomes in the GnomAD database, including 17,955 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 (17955 hom., cov: 31)
• Consequence: ENSG00000302649 ENST00000788512.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.414
• Publications: 4 publications found

Genes affected

ENSG00000302649 (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 (EAS) allele frequency at 95% confidence interval = 0.564 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
ENSG00000302649	ENST00000788512.1	n.206+37576A>C		intron_variant	Intron 1 of 3
ENSG00000302649	ENST00000788513.1	n.202-27548A>C		intron_variant	Intron 1 of 3
ENSG00000302649	ENST00000788514.1	n.201+37576A>C		intron_variant	Intron 1 of 2
ENSG00000302649	ENST00000788515.1	n.196+37576A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.482 AC: 72921 AN: 151366 Hom.: 17929 Cov.: 31

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.482 AC: 72997 AN: 151480 Hom.: 17955 Cov.: 31 AF XY: 0.483 AC XY: 35790 AN XY: 74036

African (AFR) AF: 0.571 AC: 23573 AN: 41318

American (AMR) AF: 0.494 AC: 7525 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1722 AN: 3468

East Asian (EAS) AF: 0.582 AC: 3003 AN: 5162

South Asian (SAS) AF: 0.381 AC: 1833 AN: 4810

European-Finnish (FIN) AF: 0.489 AC: 5045 AN: 10318

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.423 AC: 28729 AN: 67878

Other (OTH) AF: 0.482 AC: 1013 AN: 2102

Alfa AF: 0.408 Hom.: 7224

Bravo AF: 0.492

Asia WGS AF: 0.473 AC: 1641 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.86
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs4384980; hg19: chr3-182459069;