ENST00000739910.1:n.73+3735C>A

Variant names:

• chr5-3706083-G-T
• rs954768
• ENST00000739910.1:n.73+3735C>A

Variant summary

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

The ENST00000739910.1(ENSG00000296494):​n.73+3735C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 151,890 control chromosomes in the GnomAD database, including 5,676 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 0.27 (5676 hom., cov: 32)
• Consequence: ENSG00000296494 ENST00000739910.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 3 publications found

Genes affected

ENSG00000296494 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.307 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
ENSG00000296494	ENST00000739910.1	n.73+3735C>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41453 AN: 151772 Hom.: 5679 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.273 AC: 41470 AN: 151890 Hom.: 5676 Cov.: 32 AF XY: 0.274 AC XY: 20354 AN XY: 74228

African (AFR) AF: 0.277 AC: 11456 AN: 41394

American (AMR) AF: 0.314 AC: 4792 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1238 AN: 3472

East Asian (EAS) AF: 0.178 AC: 920 AN: 5176

South Asian (SAS) AF: 0.265 AC: 1278 AN: 4818

European-Finnish (FIN) AF: 0.289 AC: 3044 AN: 10520

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17785 AN: 67940

Other (OTH) AF: 0.263 AC: 554 AN: 2110

Alfa AF: 0.285 Hom.: 1074

Bravo AF: 0.275

Asia WGS AF: 0.234 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.40
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs954768; hg19: chr5-3706197;