rs234402

Variant names:

• chr6-4635948-A-T
• rs234402
• ENST00000716074.1:n.721+41850T>A

Variant summary

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

The ENST00000716074.1(ENSG00000284823):​n.721+41850T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0397 in 152,334 control chromosomes in the GnomAD database, including 363 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 0.040 (363 hom., cov: 33)
• Consequence: ENSG00000284823 ENST00000716074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.615
• Publications: 0 publications found

Genes affected

ENSG00000284823 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 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
ENSG00000284823	ENST00000716074.1	n.721+41850T>A		intron_variant	Intron 3 of 4
ENSG00000284823	ENST00000827010.1	n.243+11603T>A		intron_variant	Intron 1 of 2
ENSG00000284823	ENST00000827011.1	n.220+11603T>A		intron_variant	Intron 1 of 2
ENSG00000284823	ENST00000827032.1	n.231-5222T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0396 AC: 6024 AN: 152216 Hom.: 360 Cov.: 33

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0215

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.000282

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00219

Gnomad OTH AF: 0.0330

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

GnomAD4 genome AF: 0.0397 AC: 6043 AN: 152334 Hom.: 363 Cov.: 33 AF XY: 0.0386 AC XY: 2872 AN XY: 74498

African (AFR) AF: 0.131 AC: 5464 AN: 41564

American (AMR) AF: 0.0214 AC: 327 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00432 AC: 15 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.00269 AC: 13 AN: 4828

European-Finnish (FIN) AF: 0.000282 AC: 3 AN: 10630

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00219 AC: 149 AN: 68038

Other (OTH) AF: 0.0326 AC: 69 AN: 2114

Alfa AF: 0.0232 Hom.: 28

Bravo AF: 0.0452

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.6
DANN	Benign	0.83
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs234402; hg19: chr6-4636182;