4-25594195-T-C

Variant names:

• chr4-25594195-T-C
• rs939353
• ENST00000671933.1:n.343-14516T>C

Variant summary

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

The ENST00000671933.1(ENSG00000248545):​n.343-14516T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 152,034 control chromosomes in the GnomAD database, including 48,251 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 0.80 (48251 hom., cov: 31)
• Consequence: ENSG00000248545 ENST00000671933.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• Publications: 6 publications found

Genes affected

ENSG00000248545 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671933.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248545	ENST00000671933.1		n.343-14516T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.796 AC: 120969 AN: 151916 Hom.: 48212 Cov.: 31

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.796 AC: 121065 AN: 152034 Hom.: 48251 Cov.: 31 AF XY: 0.797 AC XY: 59230 AN XY: 74320

African (AFR) AF: 0.771 AC: 31962 AN: 41468

American (AMR) AF: 0.810 AC: 12360 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2735 AN: 3472

East Asian (EAS) AF: 0.889 AC: 4589 AN: 5162

South Asian (SAS) AF: 0.889 AC: 4282 AN: 4816

European-Finnish (FIN) AF: 0.777 AC: 8222 AN: 10580

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.797 AC: 54186 AN: 67966

Other (OTH) AF: 0.796 AC: 1681 AN: 2112

Alfa AF: 0.795 Hom.: 33947

Bravo AF: 0.800

Asia WGS AF: 0.885 AC: 3079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.57
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs939353; hg19: chr4-25595817;