rs4738217

Variant names:

• chr8-72180072-T-C
• rs4738217
• ENST00000803291.1:n.274+26540T>C

Variant summary

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

The ENST00000803291.1(ENSG00000304428):​n.274+26540T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,882 control chromosomes in the GnomAD database, including 13,371 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 0.42 (13371 hom., cov: 31)
• Consequence: ENSG00000304428 ENST00000803291.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.568
• Publications: 1 publications found

Genes affected

ENSG00000304428 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803291.1. 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
	ENSG00000304428	ENST00000803291.1		n.274+26540T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63140 AN: 151762 Hom.: 13359 Cov.: 31

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.416 AC: 63194 AN: 151882 Hom.: 13371 Cov.: 31 AF XY: 0.417 AC XY: 30971 AN XY: 74234

African (AFR) AF: 0.338 AC: 13998 AN: 41394

American (AMR) AF: 0.418 AC: 6391 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1657 AN: 3458

East Asian (EAS) AF: 0.399 AC: 2059 AN: 5162

South Asian (SAS) AF: 0.447 AC: 2147 AN: 4806

European-Finnish (FIN) AF: 0.494 AC: 5209 AN: 10544

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30380 AN: 67928

Other (OTH) AF: 0.415 AC: 876 AN: 2112

Alfa AF: 0.414 Hom.: 1965

Bravo AF: 0.405

Asia WGS AF: 0.419 AC: 1455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.44
PhyloP100		-0.57

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: rs4738217;

hg19: chr8-73092307;