rs6782143

Variant names:

• chr3-5726575-T-A
• rs6782143
• ENST00000425894.2:n.292-17089T>A

Variant summary

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

The ENST00000425894.2(ENSG00000229642):​n.292-17089T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0944 in 152,254 control chromosomes in the GnomAD database, including 1,286 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 0.094 (1286 hom., cov: 32)
• Consequence: ENSG00000229642 ENST00000425894.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282
• Publications: 2 publications found

Genes affected

ENSG00000229642 (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 = 0.228 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
ENSG00000229642	ENST00000425894.2	n.292-17089T>A		intron_variant	Intron 2 of 8	3
ENSG00000229642	ENST00000779001.1	n.212+30089T>A		intron_variant	Intron 2 of 7
ENSG00000229642	ENST00000779002.1	n.232+30089T>A		intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes AF: 0.0941 AC: 14322 AN: 152136 Hom.: 1278 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0597

Gnomad ASJ AF: 0.0459

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0261

Gnomad FIN AF: 0.0376

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0418

Gnomad OTH AF: 0.0898

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

GnomAD4 genome AF: 0.0944 AC: 14372 AN: 152254 Hom.: 1286 Cov.: 32 AF XY: 0.0928 AC XY: 6911 AN XY: 74456

African (AFR) AF: 0.232 AC: 9643 AN: 41528

American (AMR) AF: 0.0596 AC: 912 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0459 AC: 159 AN: 3466

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.0259 AC: 125 AN: 4822

European-Finnish (FIN) AF: 0.0376 AC: 399 AN: 10620

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0418 AC: 2843 AN: 68018

Other (OTH) AF: 0.0893 AC: 189 AN: 2116

Alfa AF: 0.0720 Hom.: 97

Bravo AF: 0.102

Asia WGS AF: 0.0330 AC: 114 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	1.5
DANN	Benign	0.59
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs6782143; hg19: chr3-5768262;