chr10-3777017-C-G

Variant names:

• chr10-3777017-C-G
• rs7005
• NM_001300.6:c.*2522G>C

Variant summary

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

The NM_001300.6(KLF6):​c.*2522G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000275 in 363,772 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: 30)
  • Exomes 𝑓: 0.0000027 (0 hom.)
• Consequence: KLF6 NM_001300.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.582
• Publications: 8 publications found

Genes affected

KLF6 (HGNC:2235): (KLF transcription factor 6) This gene encodes a member of the Kruppel-like family of transcription factors. The zinc finger protein is a transcriptional activator, and functions as a tumor suppressor. Multiple transcript variants encoding different isoforms have been found for this gene, some of which are implicated in carcinogenesis. [provided by RefSeq, May 2009]

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=-0.5).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001300.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLF6	NM_001300.6	MANE Select	c.*2522G>C		3_prime_UTR	Exon 4 of 4	NP_001291.3
	KLF6	NR_027653.2		n.3415G>C		non_coding_transcript_exon	Exon 4 of 4
	KLF6	NM_001160124.2		c.*2522G>C		3_prime_UTR	Exon 4 of 4	NP_001153596.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLF6	ENST00000497571.6	TSL:1 MANE Select	c.*2522G>C		3_prime_UTR	Exon 4 of 4	ENSP00000419923.1
	KLF6	ENST00000542957.1	TSL:5	c.*2536G>C		3_prime_UTR	Exon 3 of 3	ENSP00000445301.1
	KLF6	ENST00000461124.1	TSL:5	n.357-614G>C		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome AF: 0.00000275 AC: 1 AN: 363772 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 200594

African (AFR) AF: 0.00 AC: 0 AN: 11404

American (AMR) AF: 0.00 AC: 0 AN: 29080

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14736

East Asian (EAS) AF: 0.00 AC: 0 AN: 18510

South Asian (SAS) AF: 0.00 AC: 0 AN: 60174

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12404

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1520

European-Non Finnish (NFE) AF: 0.00000509 AC: 1 AN: 196628

Other (OTH) AF: 0.00 AC: 0 AN: 19316

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	12
DANN	Benign	0.79
PhyloP100		0.58

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: rs7005; hg19: chr10-3819209;