chr4-39123253-C-A

Variant names:

• chr4-39123253-C-A
• rs1982009
• NM_015990.5:c.*2187C>A

Variant summary

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

The NM_015990.5(KLHL5):​c.*2187C>A variant causes a 3 prime UTR 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: 31)
• Consequence: KLHL5 NM_015990.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343
• Publications: 4 publications found

Genes affected

KLHL5 (HGNC:6356): (kelch like family member 5) Predicted to enable actin binding activity. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000249207 (HGNC:58761):

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=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015990.5. 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
	KLHL5	NM_015990.5	MANE Select	c.*2187C>A		3_prime_UTR	Exon 11 of 11	NP_057074.4
	KLHL5	NM_001007075.2		c.*2187C>A		3_prime_UTR	Exon 12 of 12	NP_001007076.1	Q7Z6D5
	KLHL5	NM_199039.4		c.*2187C>A		3_prime_UTR	Exon 10 of 10	NP_950240.3	A0A804C9D6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLHL5	ENST00000504108.7	TSL:2 MANE Select	c.*2187C>A		3_prime_UTR	Exon 11 of 11	ENSP00000423897.2	Q96PQ7-6
	KLHL5	ENST00000515612.1	TSL:5	c.745-3441C>A		intron	N/A	ENSP00000425512.1	H0Y9Y5
	ENSG00000249207	ENST00000509449.1	TSL:3	n.112-2968G>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.48
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1982009; hg19: chr4-39124873;