chr3-5734900-A-G

Variant names:

• chr3-5734900-A-G
• rs7618793
• ENST00000425894.2:n.292-8764A>G

Variant summary

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

The ENST00000425894.2(ENSG00000229642):​n.292-8764A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,220 control chromosomes in the GnomAD database, including 1,919 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 0.13 (1919 hom., cov: 33)
• Consequence: ENSG00000229642 ENST00000425894.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.404
• Publications: 1 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 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.292-8764A>G		intron_variant	Intron 2 of 8	3
ENSG00000229642	ENST00000779001.1	n.212+38414A>G		intron_variant	Intron 2 of 7
ENSG00000229642	ENST00000779002.1	n.232+38414A>G		intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19253 AN: 152102 Hom.: 1908 Cov.: 33

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0718

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.0366

Gnomad FIN AF: 0.0603

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0574

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.127 AC: 19306 AN: 152220 Hom.: 1919 Cov.: 33 AF XY: 0.125 AC XY: 9268 AN XY: 74416

African (AFR) AF: 0.275 AC: 11406 AN: 41510

American (AMR) AF: 0.107 AC: 1636 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0718 AC: 249 AN: 3470

East Asian (EAS) AF: 0.178 AC: 923 AN: 5178

South Asian (SAS) AF: 0.0362 AC: 175 AN: 4828

European-Finnish (FIN) AF: 0.0603 AC: 639 AN: 10598

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0574 AC: 3903 AN: 68020

Other (OTH) AF: 0.127 AC: 268 AN: 2116

Alfa AF: 0.108 Hom.: 165

Bravo AF: 0.141

Asia WGS AF: 0.115 AC: 401 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.47
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs7618793; hg19: chr3-5776587;