5-39676175-T-C

Variant names:

• chr5-39676175-T-C
• rs4957217
• ENST00000807320.1:n.525-4419T>C

Variant summary

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

The ENST00000807320.1(ENSG00000304950):​n.525-4419T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 152,100 control chromosomes in the GnomAD database, including 59,316 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 0.88 (59316 hom., cov: 31)
• Consequence: ENSG00000304950 ENST00000807320.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 2 publications found

Genes affected

ENSG00000304950 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807320.1. 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
	ENSG00000304950	ENST00000807320.1		n.525-4419T>C		intron	N/A
	ENSG00000304950	ENST00000807321.1		n.183-4419T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.878 AC: 133368 AN: 151982 Hom.: 59279 Cov.: 31

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.945

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.952

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.877 AC: 133458 AN: 152100 Hom.: 59316 Cov.: 31 AF XY: 0.873 AC XY: 64931 AN XY: 74344

African (AFR) AF: 0.792 AC: 32842 AN: 41466

American (AMR) AF: 0.823 AC: 12561 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.945 AC: 3278 AN: 3470

East Asian (EAS) AF: 0.533 AC: 2749 AN: 5160

South Asian (SAS) AF: 0.896 AC: 4319 AN: 4818

European-Finnish (FIN) AF: 0.936 AC: 9905 AN: 10582

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.952 AC: 64767 AN: 68024

Other (OTH) AF: 0.892 AC: 1887 AN: 2116

Alfa AF: 0.891 Hom.: 12261

Bravo AF: 0.863

Asia WGS AF: 0.745 AC: 2590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.31
DANN	Benign	0.68
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4957217;

hg19: chr5-39676277;