3-123997005-G-A

Variant names:

• chr3-123997005-G-A
• rs7429448
• ENST00000801819.1:n.80+4548G>A

Variant summary

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

The ENST00000801819.1(ENSG00000304291):​n.80+4548G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,138 control chromosomes in the GnomAD database, including 1,892 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 0.14 (1892 hom., cov: 32)
• Consequence: ENSG00000304291 ENST00000801819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 2 publications found

Genes affected

ENSG00000304291 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 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
ENSG00000304291	ENST00000801819.1	n.80+4548G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21809 AN: 152020 Hom.: 1891 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.143 AC: 21820 AN: 152138 Hom.: 1892 Cov.: 32 AF XY: 0.150 AC XY: 11184 AN XY: 74382

African (AFR) AF: 0.124 AC: 5146 AN: 41496

American (AMR) AF: 0.178 AC: 2719 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 405 AN: 3470

East Asian (EAS) AF: 0.464 AC: 2397 AN: 5166

South Asian (SAS) AF: 0.268 AC: 1294 AN: 4826

European-Finnish (FIN) AF: 0.166 AC: 1751 AN: 10572

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7713 AN: 67996

Other (OTH) AF: 0.163 AC: 345 AN: 2114

Alfa AF: 0.133 Hom.: 239

Bravo AF: 0.145

Asia WGS AF: 0.361 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.52
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs7429448; hg19: chr3-123715852; COSMIC: COSV68291971;