4-38695313-T-G

Variant names:

• chr4-38695313-T-G
• rs2045767
• NM_016531.6:c.856+407T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016531.6(KLF3):​c.856+407T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 152,038 control chromosomes in the GnomAD database, including 23,231 homozygotes. 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: 𝑓 0.55 (23231 hom., cov: 32)
• Consequence: KLF3 NM_016531.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 6 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016531.6. 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
	KLF3	NM_016531.6	MANE Select	c.856+407T>G		intron	N/A	NP_057615.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLF3	ENST00000261438.10	TSL:1 MANE Select	c.856+407T>G		intron	N/A	ENSP00000261438.5	P57682-1
	KLF3	ENST00000862197.1		c.856+407T>G		intron	N/A	ENSP00000532256.1
	KLF3	ENST00000958521.1		c.856+407T>G		intron	N/A	ENSP00000628580.1

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83754 AN: 151920 Hom.: 23213 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.551 AC: 83794 AN: 152038 Hom.: 23231 Cov.: 32 AF XY: 0.556 AC XY: 41310 AN XY: 74316

African (AFR) AF: 0.520 AC: 21579 AN: 41468

American (AMR) AF: 0.576 AC: 8804 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1948 AN: 3468

East Asian (EAS) AF: 0.346 AC: 1788 AN: 5166

South Asian (SAS) AF: 0.625 AC: 3013 AN: 4822

European-Finnish (FIN) AF: 0.648 AC: 6841 AN: 10560

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38075 AN: 67968

Other (OTH) AF: 0.522 AC: 1100 AN: 2108

Alfa AF: 0.556 Hom.: 41079

Bravo AF: 0.542

Asia WGS AF: 0.504 AC: 1754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.8
DANN	Benign	0.74
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism (auto)

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: rs2045767; hg19: chr4-38696934;