5-35458373-T-C

Variant names:

• chr5-35458373-T-C
• rs1605685
• ENST00000824642.1:n.137-28330T>C

Variant summary

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

The ENST00000824642.1(ENSG00000307231):​n.137-28330T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0989 in 152,216 control chromosomes in the GnomAD database, including 963 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 0.099 (963 hom., cov: 33)
• Consequence: ENSG00000307231 ENST00000824642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 1 publications found

Genes affected

ENSG00000307231 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.229 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
ENSG00000307231	ENST00000824642.1	n.137-28330T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0989 AC: 15042 AN: 152098 Hom.: 963 Cov.: 33

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.0993

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.0903

Gnomad FIN AF: 0.0883

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.0864

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

GnomAD4 genome AF: 0.0989 AC: 15060 AN: 152216 Hom.: 963 Cov.: 33 AF XY: 0.103 AC XY: 7636 AN XY: 74416

African (AFR) AF: 0.150 AC: 6221 AN: 41516

American (AMR) AF: 0.0991 AC: 1516 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3470

East Asian (EAS) AF: 0.240 AC: 1241 AN: 5176

South Asian (SAS) AF: 0.0906 AC: 437 AN: 4824

European-Finnish (FIN) AF: 0.0883 AC: 936 AN: 10598

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0597 AC: 4059 AN: 68022

Other (OTH) AF: 0.0851 AC: 180 AN: 2116

Alfa AF: 0.0749 Hom.: 2281

Bravo AF: 0.104

Asia WGS AF: 0.145 AC: 505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	16
DANN	Benign	0.93
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1605685; hg19: chr5-35458475;