chr4-86911448-G-A

Position:

• chr4-86911448-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001414639.1(C4orf36):​c.-74+14780C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 152,080 control chromosomes in the GnomAD database, including 15,250 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 0.41 (15250 hom., cov: 32)
• Consequence: C4orf36 NM_001414639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595

Genes affected

C4orf36 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C4orf36	NM_001414639.1	c.-74+14780C>T		intron_variant
C4orf36	NM_001414640.1	c.-142-815C>T		intron_variant
C4orf36	NM_001414641.1	c.-74+14780C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.408 AC: 62027 AN: 151962 Hom.: 15255 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.408 AC: 62029 AN: 152080 Hom.: 15250 Cov.: 32 AF XY: 0.409 AC XY: 30365 AN XY: 74314

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.450

Alfa AF: 0.524 Hom.: 46792

Bravo AF: 0.393

Asia WGS AF: 0.503 AC: 1750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.074
DANN	Benign	0.34

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3113494; hg19: chr4-87832601;