rs61742835

Variant names:

• chr14-44905544-G-A
• rs61742835
• NM_001017923.2:c.927G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-44905544-G-A
• chr14-44905544-G-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001017923.2(C14orf28):​c.927G>A​(p.Glu309Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000148 in 1,353,250 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000015 (0 hom.)
• Consequence: C14orf28 NM_001017923.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.81

Genes affected

C14orf28 (HGNC:19834): (chromosome 14 open reading frame 28)

ENSG00000258949 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BP7: Synonymous conserved (PhyloP=1.81 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C14orf28	NM_001017923.2	c.927G>A	p.Glu309Glu	synonymous_variant	Exon 5 of 5	ENST00000325192.8	NP_001017923.1
C14orf28	XM_011536408.1	c.447G>A	p.Glu149Glu	synonymous_variant	Exon 4 of 4		XP_011534710.1
LOC101927418	NR_110050.1	n.161+6213C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C14orf28	ENST00000325192.8	c.927G>A	p.Glu309Glu	synonymous_variant	Exon 5 of 5	1	NM_001017923.2	ENSP00000326846.3
C14orf28	ENST00000557112.1	c.837G>A	p.Glu279Glu	synonymous_variant	Exon 4 of 4	5		ENSP00000451791.1
C14orf28	ENST00000555826.5	n.1786G>A		non_coding_transcript_exon_variant	Exon 3 of 3	2
ENSG00000258949	ENST00000555157.1	n.107+6213C>T		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000428 AC: 1 AN: 233896 Hom.: 0 AF XY: 0.00000787 AC XY: 1 AN XY: 127038

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000330

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000148 AC: 2 AN: 1353250 Hom.: 0 Cov.: 30 AF XY: 0.00000301 AC XY: 2 AN XY: 665264

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000246

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.61e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	5.2
DANN	Benign	0.79

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: rs61742835; hg19: chr14-45374747;