5-42400204-T-C

Variant names:

• chr5-42400204-T-C
• rs2972395
• ENST00000820257.1:n.347+438T>C

Variant summary

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

The ENST00000820257.1(ENSG00000306695):​n.347+438T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 152,110 control chromosomes in the GnomAD database, including 51,726 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 0.82 (51726 hom., cov: 31)
• Consequence: ENSG00000306695 ENST00000820257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608
• Publications: 1 publications found

Genes affected

ENSG00000306695 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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
ENSG00000306695	ENST00000820257.1	n.347+438T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.823 AC: 125036 AN: 151992 Hom.: 51672 Cov.: 31

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.823 AC: 125148 AN: 152110 Hom.: 51726 Cov.: 31 AF XY: 0.830 AC XY: 61685 AN XY: 74362

African (AFR) AF: 0.800 AC: 33177 AN: 41470

American (AMR) AF: 0.841 AC: 12846 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2673 AN: 3466

East Asian (EAS) AF: 0.999 AC: 5164 AN: 5170

South Asian (SAS) AF: 0.849 AC: 4092 AN: 4818

European-Finnish (FIN) AF: 0.923 AC: 9783 AN: 10600

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.806 AC: 54787 AN: 67986

Other (OTH) AF: 0.807 AC: 1705 AN: 2114

Alfa AF: 0.820 Hom.: 6645

Bravo AF: 0.814

Asia WGS AF: 0.930 AC: 3232 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.47
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs2972395; hg19: chr5-42400306;