rs6057688

Variant names:

• chr20-31390550-C-G
• rs6057688
• NM_153289.4:c.-67G>C

Your query was ambiguous. Multiple possible variants found:

• chr20-31390550-C-G
• chr20-31390550-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_153289.4(DEFB119):​c.-67G>C variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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)
• Consequence: DEFB119 NM_153289.4 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 6 publications found

Genes affected

DEFB119 (HGNC:18099): (defensin beta 119) This gene encodes a member of the beta subfamily of defensins. Beta-defensins are antimicrobial peptides that protect tissues and organs from infection by a variety of microorganisms. This gene is found in a cluster with other beta-defensin genes on the long arm of chromosome 20. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2014]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153289.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DEFB119	NM_153289.4	MANE Select	c.-67G>C		5_prime_UTR_premature_start_codon_gain	Exon 1 of 2	NP_695021.2
	DEFB119	NM_153289.4	MANE Select	c.-67G>C		5_prime_UTR	Exon 1 of 2	NP_695021.2
	DEFB119	NM_153323.5		c.-67G>C		5_prime_UTR_premature_start_codon_gain	Exon 1 of 2	NP_697018.1	Q8N690-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DEFB119	ENST00000376321.4	TSL:1 MANE Select	c.-67G>C		5_prime_UTR_premature_start_codon_gain	Exon 1 of 2	ENSP00000365499.3	Q8N690-1
	DEFB119	ENST00000339144.3	TSL:1	c.-67G>C		5_prime_UTR_premature_start_codon_gain	Exon 1 of 3	ENSP00000345768.3	Q8N690-3
	DEFB119	ENST00000376321.4	TSL:1 MANE Select	c.-67G>C		5_prime_UTR	Exon 1 of 2	ENSP00000365499.3	Q8N690-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 20

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.7
DANN	Benign	0.71
PhyloP100		-2.2
PromoterAI		-0.020	Neutral

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

Other links and lift over

dbSNP: rs6057688; hg19: chr20-29978353;