rs1374934

Positions:

• chr4-86877043-A-G
• chr4-86877043-A-T

Variant summary

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

The NM_144645.4(C4orf36):​c.*3-600T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.915 in 152,234 control chromosomes in the GnomAD database, including 64,672 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 0.91 (64672 hom., cov: 33)
• Consequence: C4orf36 NM_144645.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260

Genes affected

C4orf36 (HGNC:28386): (chromosome 4 open reading frame 36)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C4orf36	NM_144645.4	c.*3-600T>C		intron_variant		ENST00000295898.8	NP_653246.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C4orf36	ENST00000295898.8	c.*3-600T>C		intron_variant		1	NM_144645.4	ENSP00000295898	P1

Frequencies

GnomAD3 genomes AF: 0.915 AC: 139153 AN: 152116 Hom.: 64640 Cov.: 33

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.935

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.995

Gnomad OTH AF: 0.925

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

GnomAD4 genome AF: 0.915 AC: 139237 AN: 152234 Hom.: 64672 Cov.: 33 AF XY: 0.915 AC XY: 68115 AN XY: 74452

Gnomad4 AFR AF: 0.735

Gnomad4 AMR AF: 0.958

Gnomad4 ASJ AF: 0.961

Gnomad4 EAS AF: 0.930

Gnomad4 SAS AF: 0.935

Gnomad4 FIN AF: 0.999

Gnomad4 NFE AF: 0.995

Gnomad4 OTH AF: 0.926

Alfa AF: 0.982 Hom.: 115043

Bravo AF: 0.904

Asia WGS AF: 0.926 AC: 3216 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.4
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1374934; hg19: chr4-87798196;