rs6531656

Variant names:

• chr4-38682580-C-G
• rs6531656
• NM_016531.6:c.57+1898C>G

Your query was ambiguous. Multiple possible variants found:

• chr4-38682580-C-G
• chr4-38682580-C-T

Variant summary

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

The NM_016531.6(KLF3):​c.57+1898C>G variant causes a intron 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: KLF3 NM_016531.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148
• Publications: 7 publications found

Genes affected

KLF3 (HGNC:16516): (KLF transcription factor 3) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000299908 (HGNC:58760):

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=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLF3	NM_016531.6	c.57+1898C>G		intron_variant	Intron 2 of 5	ENST00000261438.10	NP_057615.3
KLF3	XM_047415764.1	c.-243+1898C>G		intron_variant	Intron 1 of 5		XP_047271720.1
KLF3	XR_925142.2	n.359+1898C>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLF3	ENST00000261438.10	c.57+1898C>G		intron_variant	Intron 2 of 5	1	NM_016531.6	ENSP00000261438.5
KLF3	ENST00000514033.1	c.57+1898C>G		intron_variant	Intron 2 of 3	1		ENSP00000421252.1
ENSG00000299908	ENST00000767350.1	n.212-7890G>C		intron_variant	Intron 1 of 1

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.42
PhyloP100		-0.15

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: rs6531656; hg19: chr4-38684201;