chr4-136060567-C-T

Variant names:

• chr4-136060567-C-T
• rs2405708
• ENST00000778051.1:n.53+3709C>T

Variant summary

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

The ENST00000778051.1(ENSG00000301335):​n.53+3709C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 151,726 control chromosomes in the GnomAD database, including 19,206 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 0.50 (19206 hom., cov: 32)
• Consequence: ENSG00000301335 ENST00000778051.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.450
• Publications: 2 publications found

Genes affected

ENSG00000301335 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.748 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
ENSG00000301335	ENST00000778051.1	n.53+3709C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75202 AN: 151608 Hom.: 19177 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.496 AC: 75279 AN: 151726 Hom.: 19206 Cov.: 32 AF XY: 0.501 AC XY: 37112 AN XY: 74110

African (AFR) AF: 0.546 AC: 22613 AN: 41420

American (AMR) AF: 0.565 AC: 8583 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1439 AN: 3464

East Asian (EAS) AF: 0.768 AC: 3961 AN: 5160

South Asian (SAS) AF: 0.573 AC: 2751 AN: 4804

European-Finnish (FIN) AF: 0.458 AC: 4802 AN: 10496

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.437 AC: 29635 AN: 67876

Other (OTH) AF: 0.481 AC: 1014 AN: 2106

Alfa AF: 0.461 Hom.: 2060

Bravo AF: 0.508

Asia WGS AF: 0.645 AC: 2202 AN: 3408

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.23
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs2405708; hg19: chr4-136981722;