ENST00000839747.1:n.99+39520C>T

Variant names:

• chr4-153799086-C-T
• rs11732581
• ENST00000839747.1:n.99+39520C>T

Variant summary

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

The ENST00000839747.1(ENSG00000280241):​n.99+39520C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0454 in 152,284 control chromosomes in the GnomAD database, including 269 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 0.045 (269 hom., cov: 32)
• Consequence: ENSG00000280241 ENST00000839747.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322
• Publications: 3 publications found

Genes affected

ENSG00000280241 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 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
ENSG00000280241	ENST00000839747.1	n.99+39520C>T		intron_variant	Intron 1 of 8
ENSG00000280241	ENST00000839748.1	n.199+9683C>T		intron_variant	Intron 1 of 6
ENSG00000280241	ENST00000839749.1	n.199+9683C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.0455 AC: 6921 AN: 152166 Hom.: 269 Cov.: 32

Gnomad AFR AF: 0.0430

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0301

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.00593

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0401

Gnomad OTH AF: 0.0597

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

GnomAD4 genome AF: 0.0454 AC: 6914 AN: 152284 Hom.: 269 Cov.: 32 AF XY: 0.0467 AC XY: 3475 AN XY: 74470

African (AFR) AF: 0.0429 AC: 1781 AN: 41540

American (AMR) AF: 0.0300 AC: 459 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3468

East Asian (EAS) AF: 0.207 AC: 1074 AN: 5182

South Asian (SAS) AF: 0.119 AC: 576 AN: 4824

European-Finnish (FIN) AF: 0.00593 AC: 63 AN: 10624

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0401 AC: 2729 AN: 68030

Other (OTH) AF: 0.0600 AC: 127 AN: 2116

Alfa AF: 0.0191 Hom.: 7

Bravo AF: 0.0463

Asia WGS AF: 0.141 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	9.2
DANN	Benign	0.73
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs11732581; hg19: chr4-154720238;